Hi,
Not sure what line cards you have or what versions of softare you are running. I have however experienced the same issue after a link flap... Everything would work fine initially then the interface would stay down after a flap and the MX line card would need to be offlined to restore service.
https://prsearch.juniper.net/InfoCenter/index?page=prcontent&id=PR1259930
After upgrading to a later version of software the optic/mic would recover after a link flap.
If you can provide more information we may be able to assist further.
Thanks
Tim