This is on 1.16 so I apologize if it is fixed already for 1.18, I saw elsewhere that you are no longer providing updates for 1.16 but I did not see this in any other reported issues so I thought I should let you know.

The stack limiter module does not appear to look at NBT data, and this behavior is not altered by the presence of a data filter module.

Setup discovered on:

Trying to keep a number of bottled sunlight and bottled darkness (from Nature's Aura) stocked in a chest. Without NBT filter will pull both items from a source chest regardless of which is set in the retrieval (or extractor module). Sum of items can reach stack limit.

Adding data filter module causes retrieval/extractor to only function on the specific item in the module confirming it is differentiated by NBT, but does not change the sum of items behavior with regards to the stack limiter.

I didn't realize but this is a duplicate of part of #175, which has recently been fixed!