That nonsense is annoying right? Happens to me 4 or 5 times a game and if I don't get the out in spite of it they almost always end up scoring.
Only thing I've done to have at least some chance to make a play is to move towards the bag and as forward as possible pre-pitch. Seems to give me more highlighted bags on certain plays. When it doesn't (which is still frequent) I've built some muscle memory and momentum control that puts me over the bag, close enough that the step to catch the ball goes over the bag, or simply a step in front of it directly on the base path giving me the tag.
I feel your pain my man, just try and be in the same spot on the field pre-pitch and get a feel for direction and length of hold to find the sweet spot. Gotta cheat the system until they fix it.