Not really. That was obviously a possibility when the separate party vote was introduced, otherwise they'd just take the local candidate you voted for and used that for your party vote. It's all an intended part of the system, based specifically on the idea of proportional representation.
Which is worse:
Under FPP, 10% of the country could support a party, but unless they won an electorate seat, they get nothing.
Under MMP, A party can get no electorate seats, but if 10% of the country support them, they get a few MPs.
I'd say the former is much worse. It's what makes a third party almost impossible in the US system.