You are absolutely right.
If you unravel the relative clause and change it to active voice, you get:
[somebody] applies for a certificate of compliance for the house.
Note that, as you rightly stated, the sentence definitely requires two fors- one relating to the house, and another relating to the certificate. Applying that to your sentence, you get:
Newly-built village houses refer to village houses for which a certificate of compliance is applied for.
That looks wrong, but it's correct if you consider the unravelled meaning of the relative clause. When the repetition of a word produces this kind of confusion, you can make it clearer by replacing one instance of a word. In this case, you could use the conjunction where with the meaning of "in this particular situation", instead of the relative pronoun:
Newly-built village houses refer to village houses where a certificate of compliance is applied for.
There is some flexibility in placement of a preposition when the relative pronoun is the object: in formal writing, you put it before the relative pronoun, and in informal writing or speech, you put it at the end of the clause. It is possible that the writer was confused by this- and I have to say that the sentence looks wrong if written correctly- and decided that there should be a preposition in only one of these locations.