Yes — this is almost certainly an autofocus issue, not an exposure issue.

Your camera’s meter and autofocus system do different jobs. The exposure meter calculates whether your chosen settings (aperture, shutter speed, ISO) will produce a bright or dark final image. Autofocus, however, needs enough light and contrast right now to detect focus. A 30-second exposure can be “bright enough” overall, while the AF system still can’t see enough to lock focus.

In AF-S (single-servo autofocus), many cameras won’t release the shutter unless focus is confirmed. In a dark scene, the lens hunts and the camera may report “subject is too dark.”

For night skyline shots, the usual fix is to switch to manual focus and focus at or near infinity, or use a bright, contrasty distant object to acquire focus first. On many cameras, the center AF point is the most sensitive, so trying that can help too.

So: overexposed meter reading and “too dark” AF warning are not contradictory — they refer to different systems.