Some friends of mine and I were dueling using some banned cards, one of which was Change of Heart. When I used it on his Machina Fortress, I should have had to discard, but I didn't. Because of this, I decided to test it with Brain Control and Big Eye. When I used Brain Control, I once again didn't have to discard. When I used Big Eye, I did.

At this point, I thought the issue was that YGOPro didn't think they targeted. This is not the case, however, because I then tested them against Yazi. Yazi's effect states that cannot be targeted. This held true with Change of Heart and Brain Control; I couldn't use them.
Not a bug. Machina Fortress's effect to look at the opponent's hand and discard a card only applies if Machina Fortress is targeted by a monster effect; that's what its text says, that's how it's supposed to work, and that's how it does work.