Probe instead of nozzle centres on the bed
TL;DR You don't need to fix it, it is by design.

When using a probe, defined the correct probe X (xxx) and Y (yyy) offsets (#define NOZZLE_TO_PROBE_OFFSET { xxx, yyy, 0 }) and having enabled #define Z_SAFE_HOMING will cause the probe to home in the middle. That is how it is supposed to work!
If the nozzle would be in the center, then you wouldn't probe the middle of the bed, but the offset from the nozzle.