I've been re-playing the game with the "Vanilla Plus" preset, and part of that is the "Item counts in messages" enhancement. However, when collecting gold skulltula tokens specifically, the message is off by one, showing +1 the actual number (including the new one).
This is on version Gibbs Alpha 6.0.0.

Here are some screenshots, just in case. (Ignore the weird item selection because of Debug Mode, this happens in regular gameplay too.)

Skulltula token count in the menu before pickup:

The message with Item counts enabled:

The menu after pickup: