DIAGNOSIS That loud clicking is almost always the sound of a stripped or damaged plastic gear inside one of the motor's gearboxes. It's a common failure point when the desk encounters resistance while moving.
FIX First, you need to figure out which motor is the culprit. 1) Unplug the desk. 2) Press and hold the down arrow until the desk is at its absolute lowest point. 3) Now, press the up arrow briefly for just a second and listen closely to each leg. The leg with the loud click is your bad motor. FlexiSpot's warranty is solid for this—you'll need to contact their support with a video of the noise and they'll ship you a replacement motor column. Swapping it is straightforward: unplug the old motor's two cables, remove the four bolts holding it to the frame, and reverse the process with the new one.
IF THAT DIDN'T WORK If the noise is more of a constant grinding hum, not a distinct click, the motor itself might be failing or there could be a loose bolt or piece of frame rubbing against the lifting column. Go over every bolt connection on the leg assembly and the crossbeam, tightening them firmly.
HEADS UP Don't keep using the desk with that noise. It will only make the damage worse and could leave you stranded at one height. While waiting for the replacement part, set your memory presets to a height you can live with, because manually moving it is risky.