There are three things that Johnson could have been referring to when he alluded to Bercow "stretching time". Firstly, and most likely, he was referring to Bercow's opposition to Johnson's attempt to suspend parliament, which went on to be challenged in the Supreme Court and be declared unlawful. Before beginning the proceedings to suspend parliament, Bercow said that the prorogation was "not a standard or normal Prorogation", and that
It is not typical. It is not standard. It is one of the longest for
decades, and it represents, not just in the minds of many colleagues
but for huge numbers of people outside an act of Executive fiat.
He also responded to Graham Stuart MP, who called his remarks disorderly, saying that
It is not disorder. I do not require advice on order from you, Mr Stuart. You are a master of disorder, man. [...] I could not give a flying flamingo what your view is.
Although Bercow's opposition to the prorogation was not the cause of it being deemed unlawful, it was certainly widely reported and may have been a factor in the eventual prolonging of the parliamentary session which led to it being the longest (839 days) since the suspension of elections during WWII.
Secondly, the Prime Minister also mentioned in his final remarks to Bercow that he was coming to the end of "what must be the longest retirement since Frank Sinatra's". It was first reported in October 2018 that Bercow would retire in the summer of 2019, however, Bercow later indicated that he would retire at the next scheduled general election, in 2022. Finally, Bercow said in September that he would retire on October 31st, or at the next general election. This could also be the stretching of time that Johnson referred to.
Finally, Bercow's handling of Prime Minister's Questions could have also been what Johnson was referring to. During his tenure as Speaker, Bercow frequently let PMQs drag on for far longer than the scheduled 30 minutes - the Telegraph reports that his final session lasted a record-breaking 71 minutes, and praises the new Speaker, Lindsay Hoyle, for wrapping up his first session in the allotted time. They also opine ironically that this was due in part to the lack of Bercow's "interminable lectures about the importance of brevity".
At the end of the last PMQs session he presided over, Bercow himself lent credit to this explanation, with his remarks given before allowing two final questions to be put to Johnson:
The Prime Minister said at the start that I had demonstrated that I
was stretching time and I would not want to disappoint him. Two final
contributions from colleagues who I know are leaving the House.
Hoyle's rather different approach was also noted in the Chamber immediately after his first PMQs session by Michael Fabricant MP, who remarked that
we went through all the names on the Order Paper for Prime Minister’s
questions and a number of other colleagues on both sides got in, and
we finished at about 12.31 pm and no one had to suffer abuse from the
In conclusion, then, Bercow was known for his unique approach to the role and attained vast notoriety as such. In particular, his handling of the unlawful 2019 prorogation attempt cemented him in the minds of some members, especially Conservative MPs, as an unacceptably partisan figure who was unfit for the role. The lengthening of the Parliamentary session that Bercow played at least a small part in, is probably what Johnson was referring to in this instance.