I watched TMP:DC the other day, and I saw a few scenes where the effects could use just a little tweaking. Looks like the blue parts on the inside of the nacelles were causing trouble. For example

1. In drydock, after the pod flies over the saucer, the nacelle on the left side of the screen looks like the blue blended into the blue screen and its has a huge black patch over it.

2. As Spock's shuttle is docking with the E, the nacelles have huge transparent areas! You can see the stars moving through them. Also, when Spock's shuttle is leaving, the stars aren't moving at all when they were seconds before.

I don't recall any others, but you could fix those two shots fairly easily if you wanted. For the Vulcan shuttle leaving, you can even reuse the same shot of the ship coming in, but matte the incoming shuttle out and insert the outgoing one.

Just in case you wanted to go "Revisited" on the movie.