Yea - the comment above cleared it up. Apparently the Cuckoo filter should have rejected the latter inserts.
As for false negatives, this can happen in both Cuckoo and Counting Bloom filters if a value that is never added is removed, and the value would have resulted in a false positive on query. The contract for removal is that you must know that the value is currently in the filter. I'll clarify that in the text.