For question 2 I think एक is a bit harder to hear because it is preceded by बिल्ली and the ई at the end of बिल्ली and the ए at the beginning of एक sort of coalesce to the ears of a non-native speaker a bit. That's just my guess. I hear the एक just fine. For question 3 One could say बिल्ली एक छोटी (I feel like this really should be छोटा) जानवर होती है। But this would be a generalized statement in the singular and would better be translated as "a cat is a small animal" as opposed to "बिल्ली एक छोटी जानवर है।" Which would be better translated as "The cat (a specific one) is a small animal". Generally there is probably some usage overlap here too.