They had nothing to do with the traitors either. Also did i mention how out of character it is for Tron to just gib someone that he doesn't like or is in his way?
Then in the poisoning of the sea of simulation scene, ... the have Tron completely unaware and reacting confused by a virus in the sea water.... Tron, the titular protagonist that is the embodiment of Antivirus software... confused.
look, maybe his definitions weren't up to date on that night, but the way they drew up complete stunned and with Clu telling him what it when he should just know that its suspicious code.
Also it's quite clear that Flynn 100% knew that Clu poisoned the Sea and was organising all those terrorist bombing on the ISOs. With that in mind, how the hell did he trust Clu all the way up to 89 with that very red flag that he's capable of murdering, organising murder and also not doing what your told for 4 extra years?
Have i mentioned this timeline is very front loaded? Almost everything happens at the beginning of the Grid with the only exceptional things going on past 1985 being Jalen disapearing and being virused then the coup and Evolution. And all of those were at the end of 89.
Oh also, the panel with a injured Tron escaping Clu's forces has this funny inking/colour error, where his arm is drawn, but the colourist filled it with ground, so it looks like he's an amputee. In the next panel you see his hand from that arm holding his chest.