Every vector bug comes in pairs. They are 180 degrees apart. If one is positive, the other is negative. If one is on-screen, the other one is behind you.

The delta-v bug shows you which way to thrust, and how much change in velocity is required, in order to get your trajectory pointing towards your target. (That will put the warp boost vector bug on your target.) And at a predefined SE speed of about 10 km/sec. (This number may vary, but usually not by very much.)

You say it didn't happen before, but that was likely when you had built up a velocity of 4,000 km/sec or so. It will take a fair bit of time for engines capable of 12.2g of thrust to slow down from that speed. You lack patience.

Trust in the autopilot (you don't have to do it in stages, the hyperjump-to does the individual steps necessary to get you on your way). Once you are on your way, you can crank up the engines if you want, to get there sooner, but any mid-course corrections may require that extra speed be negated. It will take you just as much time to bleed off that speed as you spent building it up. No free rides in this universe. And how fast you will be going when you get to your target.... :o

So getting back to this discussion of vector bugs, I should always aim for the (-) negative bug if I want to apply positive thrust to neutralize it?  So if I apply the main engines to neutralize the vector bug, whats the purpose of sync velocity?  I used both to get all the markers on target but I used the main engines first and sync velocity after that and then rotate to target for finer precision.  
I see what you mean about bleeding off speed, it doesn't actually matter if I cut the Main engines from 100 to 0 the amount of time it took me to get to my current speed is what it will take for me to get back to the speed I started at.

Looks good.

So if I apply the main engines to neutralize the vector bug, whats the purpose of sync velocity?

That is syncing velocity. It lines up the direction and velocity you are travelling with your target.

... the amount of time it took me to get to my current speed is what it will take for me to get back to the speed I started at.

You got it.

So it does stop just before hitting the target every time I dont need to slow down.  I'll just slowly approach the galaxy.  Never seen this one before so the first time I ever saw it was when I got there lol
Can I do an orbit around its center? I'm not even sure if it has a black hole there or not.

Looks good.

So if I apply the main engines to neutralize the vector bug, whats the purpose of sync velocity?

That is syncing velocity. It lines up the direction and velocity you are travelling with your target.

... the amount of time it took me to get to my current speed is what it will take for me to get back to the speed I started at.

You got it.

Oh okay, but then whats the purpose of aiming the engines and ship at the vector bug?  I thought doing that lined up the direction and velocity with the target.  I do both now to get everything lined up on the target (including the warp/boost markers.)

Cautiously approaching lol.  Now I know I have to be hands on because sometimes it doesn't stop so I have to be ready to kill warp at any moment.

I agree with all of that, but in addition, I would like to add that the answers to some of our environmental and sustainability problems may actually lie in space and what we can learn from space travel.

Trying to replicate what I did yesterday as far as lining up all the markers on the target.  I ran the ship at the negative velocity anomaly like I did yesterday and then did sync velocity, but it seems to be taking a bit longer this time.  I'm still doing this right and all the markers will line up soon if I stay on this trajectory?  And then I'll go into warp.  And is this retrograde orientation okay? I expect that will end when I go into warp?

The markers seem to be getting closer very slowly, but the Delta-V on the Warp has stayed at 32.62, is that okay?  The other two markers are already lined up on the target (that happened when I aimed the ship at the Velocity Vector negative bug.)

I waited as the markers were getting closer but the closer they got the slower they were moving so I just did a Rotate to Target instead of waiting longer and it turns out that's all I needed to do to get them all lined up.  And then Hyperjump took care of the Warp bug and looks like I'm on my way again.  Turned the main engines on (although I was moving along quite quickly even without them when Hyperjump turned on.

Sometimes SE ships and autopilots go wonky.  The info panel says it is trying to correct the delta-v of 32.62 light-years/sec. Good luck with that in your current lifetime with 12.2g engines.

Long intergalactic voyage procedure

1- aim ship engines at negative velocity vector bug until the markers move into alignment and it becomes positive and 100% efficiency is reached

2- select sync velocity to get the above markers to move closer to the target

3- select rotate to target to get all markers lined up on the target

4- select hyperjump to fix negative warp vector bug and recenter the target with all the markers and go into warp

5- select main engines as needed to accelerate to target

when approaching target hyperjump will turn off automatically but main engines will stay on......

6- slowly increase Boost exponent value to desired speed to journey through the galaxy

Doing the above my voyage from Earth to NGC 300 (6.70 MLy) yesterday took about 14 hours (getting all the markers lined up on the target was the first hour, warping there took an additional 13 hours.)

And then I spent another 4 hours or so journeying through the galaxy.....there was no central black hole but it was quite densely packed with stars!

I fell asleep around 2:30 AM again while it was still touring the galaxy, so I have to remember to end my trips before then.

*dispose of Step 3, and go right to Step 4 after Step 2, since Hyperjump will do both 3 and 4 together and from a greater distance than Step 3 will.

Sometimes SE ships and autopilots go wonky.  The info panel says it is trying to correct the delta-v of 32.62 light-years/sec. Good luck with that in your current lifetime with 12.2g engines.

lol Yeah, doing the above procedure worked though, do you think it's a good template to follow for all intergalactic trips (and in the right order?
I wanted to post some images of my trip through NGC 300 last night so here is the first one.  Notice I tweaked the Boost exponent value (step 6 in the above) to control the speed of my trip through the galaxy.  I had forgotten though that the warp engines dropped me off at the outer edge of the galaxy (since there is no central black hole) and I ended up taking 4 hours to make it through the galaxy, and probably longer but I fell asleep before the ship made it all the way through.  I was awake for the densest part of the journey, through the star clusters near the center, but tonight I'm going to try to set a faster boost exponent tonight so I dont fall asleep during the tour lol.
PS the outside view is more to my liking then the cockpit view because you get to see a much wider view of the surroundings.

This second one taken right after that comes close to matching it and I'm posting them back to back to show a sense of movement (although the warp effects already do that.)  Note my tweaking the boost exponent settings to control the speed of the trip once inside the galaxy.

And here is the first one without the HUD

The one taken right after that, to again enhance the sense of movement.

Sometimes SE ships and autopilots go wonky.  The info panel says it is trying to correct the delta-v of 32.62 light-years/sec. Good luck with that in your current lifetime with 12.2g engines.

I just did the rotate to target and everything lined up properly, and I realized I should've just done that instead of waiting 4 hours for the engines to do it on their own lol.  They did get close as you can see from the screenshots but the closer they got the slower the markers were moving towards each other but rotate to target did the trick and then hyperjump fixed the warp bug automatically.  Do you like the numbered steps I listed above as a general template for intergalactic flight?
The ship does automatically cut out of warp at the outer edge of the galaxy which seems to make cutting the engines unnecessary.  I then increase the boost a little until it gives me a suitable amount of time to do a tour of the galaxy (usually an hour or two is what I want.....I would have set the boost higher but I forgot that since this galaxy doesn't have a central black hole I got dropped off at the outer edge of the galaxy and even at the boost speed I was on, 4 hours later I was still journeying through star clusters, though I had gotten past the densest star fields, which were right near the center.  Tonight I'll set a higher boost once the warp cuts off on the outer edge of the galaxy so I can stay awake to make it through the other side lol.)