WRF output grid is smaller than input definition
Your model grid is an Arakawa C grid:


Image from Skamarock et al. A description of the Advanced Research WRF Version 3

It appears the geogrid grid generation uses the 25x25 as the furthest extents of the grid (and this is backed up by the grid maximum needing to be a multiple of the grid ratio +1).  As a result, only the u and v variables will see 25 grid points and each only in one direction, east/west and north/south respectively.  All other variables are located horizontally on the $\theta$, or scalar points in the middle of the grid boxes and there will only be 24 of these points in your setup leaving most of your grids having a horizontal dimensions of 24x24.