Hi R.,
It sounds like your son sleeps through the night. There are soooo many reasons he could be waking up upset. The people who say their kids sleep through the night and never wake up are either etremely lucky or are not being completely honest.
When kids go through any change, new development, teething, illness - they can have disupted sleep. My daughter is a pretty good sleeper but occasionally wakes up in the night. I give her a pacifier - which is pretty much the same as a bottle - it comforts her. I work full time - which it sounds like you do as well - which makes sleeping at night even more of a neccesity.
I personally used the Ferber method to transition out of swaddling and it seemed to also help her sleep more consistently through the night 8:30PM -7:00/8:00 AM. I also was very lucky and my daughter started sleeping through the night at 2 months - and I truly believe is was not because of anything I was doing - I just got lucky.
Ferber may not be the route you want to go - in the book it also referenced not starting the method if your child is sick, or mastering a new skill - such as crawling, standing, walking. It worked for me in 3 days but again I lucked out and she was already a good sleeper.
Good luck:)