What happened w/my ds was even though we used a slow flow avent nipple, it was too fast for him. (This was while he was in the hospital w/severe jaundice at 10 days old and I wasn't able to take him out, even to nurse, for 24 hrs- so I had to pump and give bottles while he was flat on his back. If I knew then what i knew now, I would have done a LOT differently). So, to prevent himself from choking, he's put his tongue up to stop the flow of milk (at least this is what the IBCLC thought after seeing us several times- she said this was the 1st baby in 16 years she hadn't been able to get to latch).
So, it's very possible it's related to the bottle, though for us, it's just a best guess, not a definite. Nursing w/an SNS if his latch is ok (my ds's wasn't) or fingerfeeding pumped milk to retrain the suck or nipple shields.
It took me a month to figure out the problem, 3 mos to fix it. My ds was also 5 weeks early, so that didn't help us, either.