I have a RB2011UiAS-RM with S-85DLC05D at one side and a RB260GS with a S-85DLC05D at the other.

After the RB260GS was turned off the fiber the Link between the two dropped and did not come back up, the RB2011 still showed the interface as running, but no data being received. If I disabled/enabled the interface then then showed as not running. After toggling the interface and auto negotiate settings and then rebooting the switch a few times the link came back up and was working fine. All settings were back to the same as they were before.

Few days later it was powered down again and the same thing happened, again the link could only be re-establish after toggling the interface and auto negotiate settings and then rebooting the switch a few times. It happened a 3rd time after this and I tried disabling/enabling the interface then reboot switch, nothing, auto-negotiate off/on reboot switch, nothing, 3rd reboot then started it working again.

The fiber has been tested, firmware on both devices is the latest, SFP settings on both sides are the default (auto negotiate enabled). I can see on the RB2011 when the fiber connection drops (unplugged or power off switch).

Is there any reason why this would be happening or something I can change to stop it?

I've seen similar things happen between different manufacturers switches using either unsupported or partially supported SFP modules.Are you using the manufacturer recommended SFP's on both ends ?

The product page for the Mikrotik S-85DLC05D says it is tested and compatible with both the Mikrotik RB260GS and Mikrotik RB2011UiAS-RM