If you're timing is on point then it's not you, its your players. Playing with the 'timing' hitting control means you have be able to ride out the cold streaks your team might go through. The game is made that way for guys who play on timing/classic.
If you want to make sure that its not you and its your team: If my team is really struggling, I go to the batting analysis screen after games and make sure that I (you the user) played well. Most games you should be
1) 45-55% percent pitches taken
2) Missing between 10-15 pitches
3) Chasing 15-20 pitches
If your numbers in those categories look on point, then you're (you the user) playing good baseball and have good pitch recognition and timing.
If you're playing good baseball and your players are popping out a lot, then its really not much you can do about it, besides know "that's baseball" and it will all even out when your players get hot.
Easier said than done, I know! And that is the reason why I play multiple franchises (3), so I can take a few days off when my teams goes stone cold, rolling over dribblers to the mound and popups everywhere. I just go play with another team for a few days.