In retrospect, yes that was probably a bad call.
However, to answer DarkSlay's query about Gligar being unable to see Skorupi, keep in mind Gligar is Ground/Flying type-not only should he have been able to sense the digging using his Flying-type sense of earth vibrations (at least once he realized that Skorupi was underground,) but he's also a Ground-type and has some knowledge of how Skorupi would be moving. In short, he wouldn't have to see you to guess you're underground. (Scary Face I'll give you, though.)
My reasoning was more for it to be out of reflex/instinct-Scary Face was an excuse, and the reflex justified the EQ. While I admit that was kind of a bad call (and circular logic), I hope my thought process has explained why I made it.
(Also, note that despite this, I still allowed Splinter to get Scary Face in.)
Either way, bringing Gligar to 13 HP despite the type disadvantage (and 4 starred +natured defense) is fairly impressive-I agree DarkSlay played well. Here's to a rematch later.