Downshifting at a stop light feels clanky. Rear Brake advice

Usually I am downshifting through the gears while holding the clutch once i'm close to stopping but still in motion. On a rare occasion I will reach a stop light and come to a full stop and then realize I only downshifted to 3rd or second gear, so then I downshift from the higher gear while completely stopped(Flat footing one leg). When I downshift while completely stopped it feels very clanky to do so. I figure the problem is the bike only wants to downshift or upshift while in motion. It only feels clanky to switch to a lower gear when I'm not in motion, otherwise it feels fine. Should I only be downshifting while in motion?

On another note, I had made a post about my brakes vibrating when I brake hard. Someone suggested I single out which of the 2 brakes vibrates. Turns out it is my rear brake. When I press it hard, and hold it there it feels like there is a vibration. I tried to make my rear tire skid a little bit but was unable to. I tried to get the tire to skid a little because I figure since I couldn't, then the vibration I am feeling might be traction control or ABS kicking in? I have the bike on Traction control 3 and Mode 3(MT-10, Mode 3 is the laziest mode). Between ABS, TC3 and M3 im not sure which of these is the reason for the rear brake vibration. I Imagine it clicks where it normally would be locking up, which to me feels like a vibration. Hoping its this and not a warped brake disc