As far as you double knee pains, could be the results of a lot of things. Might be lightly inflamed /strained, allowing undo stress.
You using new shoes, trying a different foot spacing when squatting, or jogging on ruff or uneven surfaces?
Leg extensions are used in many rehab centers, with a somewhat limited ROM.
But when locking out, and even holding that position for a few seconds can have negative affects of the joints/ligament/muscles of the knee structure. Usually happens with a heavier weight that most guy's aren't ready to handle yet. Leg extensions are not a power lift. Just a personal view, but would never suggest doing heavier leg extensions...for lifters or BB'ers.
Always a good idea to keep the knee area warm, to encourage a ample blood supply to the area, which the knee (by nature) does not always get. Heating lotions/pads/patches all good. Wearing sweats, knee warmers, etc also suggested. Taking a few weeks off from any direct leg movements may be something to consider. Rest always seems to heal a aching body part quite well.
Good Luck.