The sci-fi drama's showrunner Joel Wyman recently admitted that an early storyline from the season - which saw Peter Bishop (Jackson) erased from existence - "didn't work".
"I felt like season four had some clumsy moments trying to fudge through some of the logic leaps that you have to make," Jackson agreed, in a new interview with TV Guide.
"I was never a huge fan of the paradox that you get yourself into when you start dealing with circular time like that. [You start to wonder], if he didn't exist, how is he here, and why do some people remember him, and why is only that memory bleeding through?"
However, Jackson insisted that any unsuccessful plot twists on Fringe were a result of the show "being really brave creatively".
"You have to deal with the double-edged sword of our show being really brave creatively - that not every single one of the ideas is going to be masterful," he suggested. "When they're swinging for the fences, they're not all home runs."
The final two episodes of Fringe air this Friday on Fox in the US and will be simulcast by Sky1 in the UK.
> Fringe: A fond farewell to the sci-fi favourite
Watch a promo for the Fringe series finale below: