The winger was forced off during victory over Fulham.
O'Neil said: "I was gutted for Pedro because we did everything we could in the week.
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"He had a scan which was all clear and he was ok yesterday and he felt good today, so a tough one for me to take because it was ultimately my decision to play him and one I have to take on the chin.
I don't want it to dampen what the lads were able to produce, but we will miss Pedro and hopefully he's not out for too long."