Any possibility that the milk, bottle or teat are other than completely clean? Adding a spoonful of natural yoghurt (made from unhomogenised milk if at all possible) to the bottle can help to reeastablish the correct gut flora, and to counteract any interlopers finding their way into the feed.
Any possibility that the milk has been too hot on any occasion? They can take a few days to recover fully if this has happened.
Is it possible that milk is getting into the wrong stomach? This can happen if she is given too much milk at one feed, so that the abomasum overflows, and also if the oesophageal reflex, which closes the oesophageal groove to direct the milk into the abomasum, didn't get established, often coupled with her head being held too vertical while she is fed. (Should be just above the horizontal.)
If increasing hygiene, a bit of yoghurt, smaller feeds, checking the temperature and holding her head in the correct position don't improve things, I would put her on PFS (Pfizer Scour Formula) for 48 hours.