First off, I get the sence that you took it to an independent mechanic and not a Lexus or Toyota service shop.
A: total bullfunky. It is most definately NOT a common problem.
B: More bullfunky. If they replaced your axle(s) or even replaced just the CV boot, then the axles had to come out. To get them out, the wheel, brake rotor, brake caliper and hub nut had to be removed. The ABS sensors are fragile. If they used a sledge to get your axle out (that is common practice...not good...but common) they may have damaged a sensor ring in the either hub. If the light wasn't on before you went in and is on after you came out, something is not right and the shop most likely caused it.
Now, to give the benefit of the doubt to the shop, they may have disconnected an ABS wire so that they wouldn't damage it and just forgot to reconnect it.
Bring it back to them and give them a chance to fix it. If they don't own up to it and fix it, then tell them you will take it to a Lexus repair shop and then tell the original shop that you will take them to small claims court to get reimbursement for what the Lexus shop charged you to fix what they caused in the first place.
steviej