There's certainly old software that doesn't handle ECDSA at all, but yes you're the first I've heard of having an actual problem with software that supports ECDSA but not if signed with an RSA intermediate.
The closest I've heard of is this thread where someone was confused why a security scan tool they were using was flagging the ECDSA-signed-by-RSA signature, but as far as I could tell that was just the security scan being confused.