I couldn't reproduce exactly what you describe.
If you start with less items in your craft than allowed, I could never go into minus.
If you start with more items than allowed in your craft... then step 1 makes no sense/cannot be performed, since you already have reached maximum.
I could reproduce the minus when I started with more items than allowed in my craft.
E.g. allowed items = 10, but I already have 50 items in my craft when I start the game
When I left/right click to add more, then some item go into minus to reach the 10 limit.
E.g. if I had 20 rifles and 30 clips in craft already (together 50), and click to add more clips, game sets the number of clips to -10 (so that together we have 20 + (-10) = 10 items)
Same happens in vanilla, so it's not an OXCE+ bug.
For testing I modded the Avenger adding "maxItems: 144" (disabling any other mod but the OXCE+ extra strings).
Starting with a completely empty Avenger in Quick Battle mode:
a) I start adding rifles until I reach item limit (144 rifles) and I get "cannot add more" message popup.
b) I click "ok" to it and I'm brought back to the equipment list, showing the 144 rifles on board.
c) I still click to add more rifles and I immediately (as I should) get the "cannot add more" message popup.
d) I click "ok" to it and I'm brought back to the equipment list, but now it shows 0 rifles on board.
e) I click to add rifles and I immediately get the "cannot add more" message popup, even though it displays 0 rifles on board... (the craft looks completely empty, everything is "0").
The reset to 0 of point d) does not happen in vanilla OXC (latest nightly), but it keeps displaying 144 rifles.
Also, it resets to 0 if you're adding exclusively one item, if you have already different items on board, it reset to a negative value, which is equal to the amount of other items you have on board: so if you have 10 pistols, you reset to -10 rifles instead of 0.
Maybe there's something fucked up on my end, if some else could check this...