It's possible that he doesn't have words or understanding to tell you what he's really feeling, it could be something as benign as the different feeling of an erection. Also, as the adhesions gradually break down, it's possible that there are spots where the remaining adhesion now gets concentrated pressure on it if he was to pull his foreskin or something. It could just be the pressure on that- or if an adhesion broke away- it possible that there could be a little raw spot.
Typically boys pull their foreskin out away from their body when they are playing in the tub- and this is the most gentle way for those adhesions to be challenged and give way (as opposed to the action of rolling the foreskin back) so that's a good thing at this age.
I'm curious about the way you phrased your question about the fact that he hadn't naturally retracted yet. It's not like it just one day- boing- snaps back... retraction is almost always something that is done manually... a boy may be retractable at this age- but you'd never know it if you didn't check (don't). Don't let yourself get worried about the idea that as soon as a boy is retractable that all of a sudden a lot of washing and intervention has to be implemented- it's no big deal to just keep leaving it alone for quite some time. Eventually you will want to teach him that this can be done and that he can do it, that there is another part of his penis in there and he isn't going to hurt himself checking it out. As I said, most boys pull outward- so the idea of pushing it back can be a new one. Little kids have no idea, and some are really amazed by the discovery of their glans- so it's just a matter of giving him some information when he's a little older.
There are two parts to retraction- the adhesions releasing and the tip of the foreskin becoming mature enough to be challenged to open that wide... there is a lot of variation in when either of those things which may not happen at the exact same time.
If you aren't seeing redness or swelling, and it's just a time to time complaint and not something that's causing him distress, (like not wanting to pee or grabbing at it constantly) I wouldn't be worried about it at all.