Robin van Persie missed a penalty and also struck a post from Ashley Young's cross, while Javier Hernandez inexplicably failed to convert after Shinji Kagawa provided him with a glorious six-yard opportunity.
Rooney felt United had done enough to edge it.
"We're disappointed we didn't get the three points as we had the best chances," he said.
"Overall, however, we can see the positives. We got a clean sheet and we're still top of the group."
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