UEFA president Michel Platini said the uncertainty surrounding Fenerbahce and Metalist Kharkiv's presence in the competition over the last month, and the knock-on effects for other teams, had not been good for UEFA's credibility.
"We could suspend a team for the following year instead of keeping them from starting in the current season," Platini told a news conference.
"It is a political question. I have my views, (UEFA secretary general) Gianni Infantino has his view and the disciplinary commission people have their dissenting views."
"It is bothersome... and this is bad for UEFA's image as well," he added, referring to the uncertainty over whether some teams would be able to continue in the competition or not.
"The legal department did not spend much time on the beach this summer, rather more in the courtroom," Platini said.
"Clubs were playing, not playing, then playing again."
Turkish club Fenerbahce were kicked out of the Champions League in June, shortly before the qualifying competition started, over a domestic match-fixing case two years ago.
However, they appealed to the Court of Arbitration for Sport (CAS) who provisionally reinstated them and they were readmitted at the last minute.
They then beat Austrian club Salzburg in the third qualifying round and faced Arsenal over two legs in a playoff with a final decision still hanging over them.
In the end, Fenerbahce lost the Arsenal tie and their appeal, which meant they missed out on the Europa League for which they had qualified, allowing APOEL Nicosia to replace them in Friday's draw.
Salzburg also lodged a protest with UEFA, which was rejected, before they appealed to CAS which has yet to issue its final ruling.
Ukrainian club Metalist Kharkiv also went to CAS after being banned for match-fixing although, unlike Fenerbahce, they failed to gain provisional reinstatement and eventually lost their appeal.
Their absence again forced UEFA to make a last-minute switch, replacing them with Greek side PAOK Salonika as Schalke 04's opponents in the Champions League playoffs.
"It was a tough summer, a bit complicated between disciplinary committee appeal procedures, CAS and all sorts of things," Platini said.
Infantino explained that UEFA could act retrospectively on any proven incidents of match-fixing dating back to April 2007, when the disciplinary statutes were altered.
It would only take action, however, once a team had qualified for European competition.
The policy could potentially affect Italian clubs Torino, Sampdoria and Atalanta, who have all had points deducted since 2007 over match-fixing cases.
"One of the tasks of our integrity officers is to feed UEFA with information so we are informed about what is happening in every country and then, depending on what happens in the future, UEFA will have to take decisions," Infantino said.
"In the Fenerbahce case, there were thousands of pages in Turkish which had to be translated before the disciplinary committee decided to exclude them."