I noticed this as well; however, when I went to go and try to fix it myself, I couldn't find any reference to any part of GameTooltip:SetOwner, or even tooltip in general, in any of aguf's lua files. (I searched using Windows's Explorer's search, for *.lua files GameTooltip, SetOwner, or just Tooltip in them.) I'm guessing, then, the problem is more complex and has to do with something the Blizzard UI is trying to call from the aguf frames, which isn't being passed correctly? I do use TinyTip, but the problem persists when only aguf is loaded anyway.
Overall the issue is minor for me. The frames still work as normal, and because I run !ImprovedErrorFrame I only ever get the first error report in the chatframe (which can be disabled in the default Interface options), repeats of the error simply incrementing a count in IEF's button icon.