It's important that he empties one boob (even if it takes him several tries over a couple of hours) before he gets the next one.
Was the bottle EBM or formula? Trying an EBM bottle would perhaps split issues due to chemistry/intolerances from issues due to way-of-eating.
If he is gaining weight happily then he's getting enough milk - if not then hunger may be part of it, and measures to increase milk supplly may need to be considered.

Feeding with him more upright may also help - it may be that this was easier to do with a bottle...But it is possible to do with bf as well (generally a football-style hold with bub on a slope).