Can an invalid Omni transaction be confirmed by bitcoin miners? Is it possible that a well formed Omni transaction (with valid Omni layer data) be valid for Bitcoin miners while being invalid for the Omni token being used ?
Yes, Bitcoin miners don't perform any validation beyond the Bitcoin validity rules. Omni transactions rely on OP_RETURN values, which don't matter to the Bitcoin miners. 

As long as a tx is a valid Bitcoin tx, miners are free to include it in their blocks.

When an omni node sees such an invalid transaction, it will simply ignore any asset movements the tx claims to perform.