I don't think your notary misadvised you. In order for your wife to own a specific part of the property, it has to be defined, so you need a 'projekt wordrebnienia lokalu' - basically a document from a licensed architect that the property is self enclosed (i.e. it's not half a room, or a couple of rooms in a larger flat etc) and that it has its own entrance. This can then be stamped by the relevant authorities (from memory, the architecture office but I could be wrong) and accepted by the notary as proof of what your wife is going to own.
does he have any legal grounding to challenge her and her brothers 1/4 allocation or at the parents death would their 1/2 have to be split among the 3 children?
Has the paperwork for the 1/4 been signed and sealed? If so, why would he challenge her allocation if he's left with half of the property in the will? He ends up with half, they have a quarter each... If anything, your wife and her brother would have the right to claim a zachowek.