I don't think this is a bug, this is a feature.

Fees make transactions have different speeds, thats is the whole point of fees (at this point).
The bigger the fee, the faster the transaction (theoretically).

A second transaction with hier fees can go faster and possibly reach 51% of the network faster than the first transaction with no, or lower, fees.

As a merchant you should look at the fee paid for any given transaction, and allow more confirmations for lower fees,
I dont think there is any other way around it, since mining operators will always prioritize higher fees.

I think, that ideally, a 0 fee transaction should wait for 51% confirmations before being acted upon.

Does any of this make sense to you?