First (oops, our condiment-eponymous friend beat me to point 1), true the wheel, or get it trued. It's easy to let a wheel without rim brakes go out of true; with old-school brakes you'd have more incentive. In your case, the incentive is the fender. Tight clearances call for a trued where.
Second - is this a quick-release wheel? If so (actually, even if not....), check that the axle is centered in the dropouts. If it's not, that will "cock" the wheel left or right, which may be what you're seeing with the uneven clearance.
Another possibility, should NOT be the case with a new-ish bike, but you never know..., the rim may not be centered between the axle locknuts. One poor-man's way to check that is to put the wheel into the frame backward. **NOTE / DISCLAIMER** I've never worked on a disc brake bike, so unless you're sure there's clearance to do this, on BOTH sides (rotor on the drive side, cassette on the caliper side), don't try this. Maybe someone with disc brake experience, who has tried this trick, will chime in. Anyway, imagine if the rim is not centered between the outer nuts on the axle. That would cause the whee to run too far left, or too far right, between the stays. So what happens when you mount it the other way? If indeed this is the issue, the phenomenon "reverses" itself. In your case, instead of the tire being too far left, it'll be too far right. That would mean either the wheel is not _dished_ properly (refers to relative distance between the hub flange and the rim, left vs. right), or the spacers, washers, etc. on the axle are not arranged properly.
If reversing the wheel doesn't change anything, then you're back to the fender still not being centered, or possibly the axle not really even/straight in the dropouts. Or even (again, should NOT be with such a new bike, but you can't assume....) the possiblility of the rear triangle not being straight.
Did you get a look at how the tire sits between the stays, before installing the fender? It'll be hard to tell with the fender in place, but "bare naked", you can probably eyeball whether the wheel rruns centered between the stays.