Nikon’s manual-focus confirmation uses the camera’s AF sensors, so it can be affected by the same calibration issues as autofocus. In practice, AF Fine-Tune can shift where the camera considers focus to be, even when you’re focusing manually.

What you can do:

• Use the camera’s AF Fine-Tune menu and test at wide aperture so depth of field is very small.
• If focus is consistently in front of the target, apply a positive adjustment; if it’s behind, apply a negative adjustment.
• Repeat until the confirmation indicator better matches actual focus.

Important limitation:

• For CPU lenses, Nikon can store AF Fine-Tune values per lens.
• For non-CPU/manual lenses, the camera usually can’t store a separate value, so you may need to change the global/default AF Fine-Tune setting, which affects all lenses.

There’s no commonly available user software specifically to recalibrate only the confirmation dot itself. If the mismatch is significant and you want a deeper adjustment, Nikon service may be able to calibrate the body/lens more precisely than the user menu allows.