Imagine a language with verbs having slots for both subject and object markers, thus:
Oh, this language is ergative, btw, so
is maybe more accurate.
Let's further imagine that certain other things go on the verb, e.g. negation. Let's further imagine that negation (and maybe something else) occupies the object slot, and intransitive congruence moves to the ergative slot, whereas objects of transitive verbs just don't get congruence at all. (Consider how, for instance, subjects don't get congruence on the main verb at all in negative clauses in certain Finnic languages – having this for objects seems even less weird, really.)
Now we've created a situation where the ergative is the nominative in negative clauses, which iirc is typologically uncommon. In fact, the ergative serving a nominative role in splits is generally speaking uncommon.
Other things than the negative might occupy the same slot.