Yes. As per Rule proviso in Rule 46 of CGST Act ,it mandatory to sign Invoice . Shall not be required sign if issued electronic invoice as per IT Act .
Hence the penalty can be levy on invoice without Signature
Legally speaking, the Invoice should be Fully compliant with rules... but practically there might be atleast some glitches here and there.. If the transaction is genuine, go ahead with whatever you're rightfully doing, because Invoice would be scrutinized only when you're under scrutiny