I have seen TSA screeners tell pax to put flip-flops back on rather than put them in the bin: at JAX, SAN, and MYR, to name a few.
I have also personally been told, "Those must come off," when wearing flip-flops at IAD and RDU, and at CRW was told I had to remove my leather sandals. (and to settle debates, the phrasing was "must," not "recommended," with the screener physically blocking the WTMD)
I did once see one of these same screeners doing different duty (at the x-ray) when her co-worker let me through wearing tennis shoes without a word. The look she shot at me when I complimented the guy and at the WTMD guy himself that day was lethal!