Here's something to know. When medals award in-game they do not award on your profile at that time. In order to get them on your profile, reload the game and (re)play a level or two and wait around a bit. All 5 medals required this!
I would also suggest no more mine cart levels in any future games. I understand you are most likely taking inspiration from the Donkey Kong Country series (or maybe Pac-Man 2?) and it worked in those games, but those were by far the worst of the levels in this game.
In fact one of the mine cart levels (Secret 42) I'm not sure is possible because you put a red block that is way too high to jump but too low to roll under right up top of a steep incline before the trophy.
Fortunately the game bugs in the counting sometimes, such that it gives you more levels completed or more secrets completed than you've actually completed. That was nice because for example I'm not sure that (Secret 42) is doable as-is so that helped out. It seems to only bug in favor of the player, which is nice.
It's probably not a bad idea to give the player a tiny amount of wiggle room anyway and not require absolute 100% completion on a game of this difficulty. Anywhere from 95% to 98% should be "good enough". With how many stages there are and how difficult they are, this isn't unreasonable and it's not without precedent.