I report a issue with Fiber Cloud Routers (ccr1016-12s-1s+) and fiber CRSW to MikroTik since 1 month ago.
Don’t use OSPF and BFD or you will have a lot of intermittence not caused by your links.
This is a known bug.
It will not be fixed until RouterOS v7 
Can’t wait for that to to get fixed so we can use MikroTik in Telco environments that have to meet SLAs in the milliseconds.
No one knows when v7 will be available. Mikrotik should disable BFD in fiber equipment until fix it.
I have to move some equipment to Ubiquity Edge Router who has less CPU but enough swappable RAM for run my actual topology.
@Mikrotik don’t let engineers suffer with this issue. People try this in lab environments but never imagine that a fiber equipment will have a issue. That cost me several thousand of dollars.
Until know I have to move also a CCR1016-12S-1S to another manufacturer since I really need BFD for OSPF and BGP. I can’t find anything that be so cost effective like Mikrotik. Any suggestion?.