He might have reflux and lying him flat might give him reason to wake up, with sore tummy or heartburn.
If he likes to be swaddled, swaddle him tightly. Put him in a vibrating boppy chair so that he almost in a almost sitting position, but lying on his back (make sense?) put this in his crib and have the camera pointed at him so you can keep an eye on him (crib railings up of course). Don't put the vibrate on, just swaddle and let him ly in it, if you have to softly bounce it for 10 min or so, and if he will sleep do that again next time but shorten your time, doing that every night until he is happy to just sleep in there. See if this helps.
My son was a tummy sleeper.. and slept much better when I decided to go against everyone's advice and let him sleep on his tummy... just make sure there is nothing in the crib that could suffocate him. (Teddy bears, blankets strings, and take out your crib bumper and replace it with a mesh bumper, they fasten with valcro and have no strings to tie, plus it allows better air flow). The camera monitors are so good.. Just LOVE them... Keep an eye on him as he lays on his tummy, you can get an idea if he likes it or not.
A tight swaddle is always good, and make sure he gets enough to drink so he does not wake hungry.
Wet diaper might also wake him, thinking about giving him milk as stated above... so a good night time diaper.
usually it is 5 things that wake babies up
1. Hungry
2. Wet
3. Gas (Burping, walk around the house with him in a bouncy step)
4. Needs to be swaddled
5. Feeling sicky (Cold or tummy bug)
so remind yourself of these 5 things when he wakes.. and soon he will go back to being himself. And hopefully you can get some rest.
hugs