I'm homebrewing a magic shortsword, and I added a second spell to it that is supposed to use the charges. Yes, before you say anything about it, I made sure the min-max charge boxes were filled out.

The problem is that now in the character sheets, it shows that the spell is granted 'at will', and when I tried to delete the spell off of the item, even after saving, the spell was still on the item even after refreshing the page after waiting for several minutes. I tested this with the second spell I had put onto the item, and it had the same result. I can only gather that this is a bug with the homebrew magic items.

So what are the specific details, like what spells, how many charges, cast at what level, etc. I can then see if I can replicate the steps. 

My suspicion is you're just doing it incorrectly, but without know what to replicate I cannot test.

Did you add the charges to the item?