I created an amulet that lets the user cast See Invisibility at 2nd level. I set the item to have 2 total charges that reset after a long rest. Then I added the actual spell with a Minimum and Maximum use of 1 charge.

The item gets added to the character correctly, and the spell shows up in their spell list to use. However, it is always set to consume two charges on the item, rather than the one charge I set. It also does not reset the charges after a long rest is taken. Is there another step I should be taking? Right now, the workaround is to just manually edit the item which can get bogged down by plenty of other tasks.

Ensure Cast At Level is set to 2.

Items cannot be set to automatically recover charges. Resetting charges on any magic item, official or homebrew, must be done manually on the sheet. This is a known limitation of the system.