The last-32 fixtures each saw delays, with Roma's 2-1 victory over Feyenoord marred by apparent racial abuse of Ivorian forward Gervinho after an inflatable banana was thrown in his direction from the stands.
After French referee Clement Turpin ordered an announcement calling for fans to stop, play eventually resumed, although he was forced to take the players off the field in Rotterdam in the second half after objects were hurled in his direction following the dismissal of Mitchell te Verde.
Roma eventually progressed 2-1 - Gervinho hitting the winner - following the highly charged second leg, with the reverse fixture in Rome having also seen trouble in the Italian capital.
Guingamp's exit at the hands of Dynamo Kiev also saw delays after home fans invaded the running track around the pitch, apparently in response to an inflammatory flag on show in the away support.
With home fans attacking match stewards, veteran goalkeeper and Dynamo captain Oleksandr Shovkovskiy was forced to intervene in an attempt to calm the tense scenes.
The incidents in both games are likely to be the subject of UEFA investigations in the coming days.
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