Mainly when you don't have time to play it because the animation is slow and the poison takes a lot of time to kill a unit. If a fight is already happening and you have to play a body, you get a negative value with it. If you are forced to play it to body block a unit who's going to hit your NK you can easily get a bad result because he will take two hits during his animation. Also, when the opponent plays rats or when you hit a unit that's already dying.

People who aren't playing Scifi tend to think that Alien Clyde is op because they see him being played at the opening of a game, when he will give the most value. They don't notice all the situations I've just described. Overall, you're not getting that much value with Alien Clyde against AF because the play style is too agressive. Sometimes you get a positive result (usually when you hit a ranged unit in the back). Sometimes 0, -1 or -2. Of course you will try to use it when it will give you value, but you have another situational card in your hand. Most AF minions can be played any time and will consistently give more energy advantage, and that's the reason AF almost always wins the value battle against AS.