I have three CRS354-48G-4S+2Q+, every of them on its floor. But one of them acts very strange. I cannot connect to it using winbox and IP address, when I connect using mac address, it looks good, but disconnects couple of times. Sometimes I can even connect using IP address, but mostly not. I cannot see anything weird in logs. Pings are OK, no packet loss.

What do I have to check ?

If you can see it and sometimes connect i'd start by look at CPU utilization and traffic. Maybe it's just overwhelmed by heavy load or mis-configuration.

Winbox says Connection refused. Which is weird. No errors in logs, CPU load is fine.

can be other device is trying to use same switch ip address?

check in your PC ARP table to see which mac address is responding to intended ip address requests

Well when I look to winbox neighbors I can see quite different mac address than I can find on my laptop using arp -a

Of course mac address showed in winbox is correct, on my computer is not correct. I am trying to figure it out what mac it is and why.

You mean that the Winbox neighbors table shows one combination of MAC address and IP address for that CRS, and arp -a shows another MAC address for the same IP address? If so, Winbox access via MAC address to the CRS should nevertheless work, so it's not the only problem.

In any case, https://macvendors.com/ may help you find out what device has the same IP address like the CRS.

Also, given how sensitive Winbox is about short-term outages, you may want to try to connect to one of the other CRS machines and use /tool mac-telnet to connect to the problematic one using command line from there, to check its status (CPU load etc.).

I can see quite different mac address

How different?

If it's the same except for the last octet, that's normal. Each port on the switch has a different MAC, and you may be connecting to a different port in each case due to bridging. The addresses assigned to a given switch will be in order, so they differ only in the last octet. (This issue can play havoc with static DHCP assignment.)

If it's entirely different, then do an OUI lookup as @sindy suggested to get a hint at who is answering your Windows box's ARP request. You may have a router between you and the switch, and its MAC will be the one you get. (I use Wireshark's online OUI lookup tool instead.)

Using https://macvendors.com/ I found out the mac address I am getting is from RaspberryPi.

I found out one of my collegue placed some RPi which has conflicted IP address with CRS354-48G-4S+2Q+. But it was not so easy to find out what is going on and where is that device and who is responsible for

Sorry and thanks for all helps