My 6 Month old has just learnt to crawl and has started to rock back and forth in his cot at night. He generally sleeps on his side or tummy (but is always placed in his cot in his back). The last few nights he has started to toss and turn and smash his head against the side of the cot, and also rock back and forth on his tummy and bang his head up against the cot bed head and wake himself up from hurting himself. Is there anything I can do to stop him hurting himself? I know bumpers aren’t recommended, is there anything else I can put on the cot to make the sides softer so he doesn’t hurt himself?

Your are correct, Red Nose does not recommend the use of bumpers (or any soft padded items) for baby in the cot.

It is not uncommon for babies to roll into the sides of the cot hit their head or get arms/legs thru the slats.
Most bumpers do not cover the entire sides of the cot & may (or may not) reduce the impact.

Raising Children Network has the following information:
It’s common and normal to see young children body-rocking, head-rolling and head-banging at bedtime or during the night. They do it because it’s rhythmic, and it comforts and soothes them.
Body-rocking often starts around six months of age.
https://raisingchildren.net.au/preschoolers/sleep/night-time-problems/body-rocking-head-rolling-head-banging#sleep-issues-body-rocking-head-rolling-and-head-banging-nav-title

Are you still wrapping (or using a swaddle suit with arms in) your baby? or is he in a sleeping bag? (with arms out)
Do you think he might be cold?
Is he getting bruises?
If you are concerned about him injuring himself, then it is important you talk to your GP or Child Health Nurse