I've noticed this for a while, but the last couple of times in the theme they say "Three's Company Too!" they are really saying:

Three IS Company Too

I even turned on the closed caption, it even put it down as the words!

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Shirley: Well, now you've done it, haven't you? You have crumpled the universe!
Laverne: I crumpeled a leaf!
Shirley: You can not see beyond the obvious, Laverne! If you could, you could see the forest for the trees, you would see that on those trees grows the UNIVERSE!
Laverne: On those trees grows a LEAF!

ALF: As Barry as my witness, I'll never go hungry again!