OK, but my experience at any checkpoint that has CLEAR is that once they verify you they escort you to the front of the Pre line (which I feel slightly bad about at e.g. SJC terminal A because the Pre line is all the way across the setup from the Pre side and they have to undo like 4-5 tensa-barriers but I'm not the one who laid it out...)

If Pre was open and they didn't do this for you, complain to CLEAR.

If Pre wasn't open at that checkpoint at all, the you wouldn't have had it either way.

Unless JFK T4 is one of those places that has a dedicated lane for people who have both (I forget if it is -- this seems like something we should collect in a wiki somewhere)* and you mean that you inadvertently got in the CLEAR-without-Pre lane when there was a CLEAR-with-Pre available? (Although in those cases where I've been about to do the same thing they've usually redirected me to the other one.)

*EDIT: Clear appears to make this distinction on their web site, eg. DTW:

https://www.clearme.com/where-we-are/dtw

"CLEAR Lane and Enrollment for Precheck-eligible travelers"

vs. at other locations, merely "CLEAR Lane and Enrollment"

JFK T4 indeed has a "CLEAR Lane for Precheck-eligible travelers" with hours listed as 4a-8:30pm, and "CLEAR Lane for standard security" 24 hours.