I tested it and the same thing happens with seeping heart, mutated arm, mutated leg, etc. Basically all the comestibles with type food and use_action mutagen

The problem is in avatar_functions.cpp in the void use_item( avatar &you, item &used ) function

A mutagen like lupine mutagen is inside a flask, so the item is glass flask, and the glass flask returns false on used.type->has_use() so the item goes here and it gets consumed

    } else if( !used.is_craft() && ( used.is_medication() || ( !used.type->has_use() &&
                                     ( used.is_food() ||
                                       used.get_contained().is_food() ||
                                       used.get_contained().is_medication() ) ) ) ) {
        you.consume( used );

But the putrid heart returns true on used.type->has_use() so it goes here instead

    } else if( used.type->has_use() ) {
        you.invoke_item( &used, used.position() );

I tried to add more checks on bool Character::invoke_item( item *used, const std::string &method, const tripoint &pt ) on character.cpp

if( used->is_tool() || used->is_food() || used->get_contained().is_food() ||
        used->is_medication() || used->get_contained().is_medication() ) {
        return consume_charges( *actually_used, charges_used );
    } else if( used->is_bionic() || used->is_deployable() || method == "place_trap" ) {
        used->detach();
        return true;
    }

And that causes it to consume charges as it should but then it doesn't show the message that says "You eat your x", and I don't know how to fix it properly

Edit: I think I got it but I'm gonna wait on another PR