Thank you for playing and leaving a comment! Glad you enjoyed it :)
I think you might have missed one optional missile expansion back in the swamp area past the plant boss (you need the water mobility upgrade to be able to reach it). Other than that, it sounds like you got everything. Congrats! :D
Hmm I did run into a similar issue towards the end of the jam where upgrade items were respawning , but thought I had fixed it. I'll look into it and make sure to patch it out in future iterations of the game.
Thanks again for the feedback! :)