I've had my new Mac Studio Ultra set up for around 48 hours now and have been experiencing these same issues. It's been fairly inconsistent and I haven't been able to recognise any patterns yet as it's still too soon, but it's been happening enough for me to have searched for a thread like this.
I should start by saying that I have x2 Benq 32 inch displays connected, a couple of LaCie portable disk drives, a Magic Keyboard and a Logitech MX Master 3.
Another really annoying problem I've been getting frequently is that when I wake the displays, I find many application windows have been scaled down into the bottom left-hand corner of the main screen.
Sometimes the Mac Studio and displays will wake immediately after going into sleep. Other times, the Mac Studio does appear to go into sleep mode, but I notice that the connected disk drives keep waking and spinning up, then going back to sleep again … but continuously. I've also noticed at times that even though the displays haven't woken, the fan in the Mac Studio is running, so it's not really sleeping.
I've tried sleeping with Bluetooth turned off, but it didn't appear to resolve anything. However, just before this I did switch off the Logi MX3 and then the Mac did go into and stay in sleep mode. I have tried adjusting the energy savings prefs, but I haven't found a combination that makes any difference. Usually I check Prevent Mac from automatically sleeping and un-check Put hard to sleep etc… I don't want the external drives to sleep whilst the Mac is on, but instead I want them to sleep when the Mac is asleep, but this doesn't seem to be happening.
If I have to leave the Mac on 24/7 then so be it, but the thing that's really frustrating me right now is this problem with application windows bunching up into the corner of the screen when the displays wake. I previously had one of these displays connected to my iMac 2020 and never had any issues of the sort, so I don't think there's any problem with the display itself – I also have another one connected to my iMac Pro and again, no issues with it.
Edit… in fact, something I'm noticing just as I sit here typing is that even though I have un-checked Put hard disks to sleep when possible, my two LaCie USB-C drives keep sleeping and waking, like on loop.