Tore his ACL during the Max fight. He called GSP to ask about his surgeon and GSP past on the details and even flew out to LA to see how Conor's recovery was going. Just highlights what a great person GSP is.
Conor partially tore his MCL in the lead up to the Aldo (and then Mendes) fight. A fighter got a little too over zealous grappling. It's not a huge deal but it does take away your stability with certain movements and then in turn your strength. You can see during some of Mendes' take down attempts - once the weight shifts to Conor's bad knee he gives up the takedown. It's a 6-8 week injury and doesn't require surgery (especially when factoring in his age). It's part of the reason why he said the Ultimate Fighter timing was good too as he could stay and rehab with Arnie's physio (she helped him for the Mendes fight).
The reason he doesn't do a tonne of roadwork as it's bad for the knees and it isn't efficient. There are better forms of training now. Look up HIIT. Same benefits in less time. It just makes sense to shift to that style as MMA is short duration bursts and you need to recover quickly. People act like you need to pound the pavement over and over to get results but it isn't the 50's any longer. Some athletes will never have the endurance of say a diaz brother and that's largely due to their fast/slow twitch muscle fibre types. Really basic physiology.