First you are not doing anything wrong. What you are describing is totally normal. Day sleep and night sleep are totally different sides of the brain.
In an infants sleep cycle there are exact partial awakenings at the 10 min, 20 min and 40 min marks of young infant sleep. When you are teaching sleep, be prepared to support your newborn/young infant, so that these partial awakenings don't become full awakenings back to consciousness. Shielding eyes, body contact/pressure will help. Stay with your little one until past 20 mins.. even if you think she/he's completely asleep. As your little one gets used to falling asleep and staying asleep past these jolts.. you won't have to stay as long.
It sounds like he is having trouble with the awakening at the 20 min. mark-- which sends an infant into full deep sleep. It's a bit of a jolt, and if he is really overtired, this jolt can cause him to cry out and fully wake up. So, once he is asleep, stay in or near his room and wait for the stir at 20 mins. Put your hand on him to help him settle-- but be as subtle as you can, just let the pressure of your hands settle him. In fact, I would put my hand on him before the jolt. Be prepared for the first few naps to be tough, because he is used to fully awakening at this point. This isn't something that will be solved in a day.. more like a few weeks. But if you are consistent and persistent, he will get past it.
Lastly can't see if you said you swaddle, but it will help w/ the jolts greatly. So swaddle tight!, Dark Room, white noise and be prepared to help dc thru the sleep cycles.
Hope that helps! We are here for support if you need it! :wink: