I wouldn't get to alarmed to soon. You're back training in a way the body isn't use to. The knee mechanics are now different to pre ACL injury and they need to get used to the new joint movement (or lack there of). If you had Wikipedia reference-linkmeniscus removed at the same time you could have some bone on bone issue.

Really you can't go from basic rehab, even gym, back to game readiness. Running and agility drills are an essential part of the full ACL rehab program and should be done to a fairly pain free level (with good guidance) before training for an actual game beings.

Perhaps you've missed some of that rehab and now the knee is feeling the shock of jumping up a few gears. Give it a little time but perhaps back off a little and get a post exercise opinion from the local PT.