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Yeah, almost certainly an alignment issue.
@nejib have you tried undoing the caliper bolts and re-aligning the caliper? Worth taking the pads out, give them a light scrub with sandpaper and reinstall.
Is the noise constant or only when applying the brake?
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It was only when braking, plenty of clearance. I had already cleaned rotors with iso and sanded pads. Realignment seems to have got rid of the clicking noise, just back to a "contaminated" sound so maybe new pads in the future or a long ride through the mud. Thanks to you and @coventry_eagle for the replies!
Bent rotor? Rotor bolts not tight enough? Misaligned caliper? Unevenly worn pads? Loose caliper bolt? Worn pads?
Nope, holes in rotor isn't the issue.