Number 1, you shouldn't have cut the yarn but taken it back to the store immediately to show them what a mess their clerk made.
Two, you should still TAKE the whole thing back to the store. Talk to the owner/manager and tell him/her you just want to make him/her AWARE of the situation and perhaps they should train clerks to use the winder CORRECTLY. I wouldn't demand a refund or exchange or anything. Emphasize that this visit is informational for them. MAYBE they will offer you a replacement or a credit or something as a good will gesture. If they deny any responsibility, are rude or say its all your fault, tell them in no uncertain terms that you will find a new lys or just shop on line. (Brick and mortar store owners hate it when you say you're going to shop on line.)
Third, go to the to basic techniques videos (above) and under "More" scroll down and watch the vids on joining yarns so in the future you can avoid the knot thing. If the yarn is 100% wool, you could spit splice it together. If it's superwash or not all wool you could use the russian join or the knitted in join. Both are simple and the yarn won't be a total loss. Any of the joins would be more comfortable than all the knots.
As frustrating as this may be, you gotta think of it as a learning situation. Imagine, you'll know how to join in new yarn in you sleep. Color work will be a snap.