During the TV series:
Anytime Kirk sleazed over a woman.
Anytime Wesley saved the day.
Time wasted on Pulaski.
The moment Neelix appeared on screen (with the knowledge that he wasn't going to die in the next scene).
Anytime Seven saved the day.
Everytime Archer opened him mouth.
And for the films:
Taking forever to switch on the lights around the Enterprise
Attempts at humour or bad language in TVH (sorry, but always makes me cringe).
All of TFF.
Uhura not being able to speak Klingon in TUC.
Data's "Oh Shit" in GEN.
'Slow things down' in INS.
In NEM: Wesley back in uniform with no explanation, Worf back in uniform with no explanation, the driving scene, Troi having to use Worf's hand to target weapons (she could have done it just as easily herself), B-4 becoming Data 2.0.
Any scene where there were camera flares in Nu-Trek.