When I took the Chemistry subject test, I got a 650 which is in the 40th percentile. Will this look bad if I send this to a Ivy?
Yes, it will look bad if you sent it to an Ivy.
If your 650 is accompanied by two 750’s plus and maybe you decide to retake SAT II Chemistry, it’s no big deal. You need to be more specific, what other tests did you take and what was the score?