The question isn't exactly accurate. Quorra didn't say they couldn't go off the grid - just that they could not follow them. When she rescues Sam, they jump the vehicle across a canyon and switch the vehicle into all-terrain mode. The light cycles that were used in the games could not follow them or make the jump, but CLU has no problem traveling into the badlands or other parts of the grid.
Flynn was not hiding off the grid. He was hiding in the badlands which was outside the city. CLU didn't know where Flynn was because he disappeared after the war. Staying in his hideout, his approach to fighting CLU was to do nothing.
Had CLU known about Flynn's whereabouts he would have gone there and forcefully taken Flynn's disk (but he could not kill him, as the two were the same). Since Flynn had disappeared, CLU tricked Sam into entering the grid in order to get Flynn to expose himself.
CLU was able to trace the light cycle back to the hideout, because light cycles leave a trail behind them. It's this trail that is used to create a wall of glass in the games. Had Sam used a different vehicle then maybe CLU wouldn't have been able to retrace its path.