The inconsistent image flag warning happens whenever you have bonds in a data file where the distance between unwrapped atom positions is larger than half the box length in x-, y- or z- for periodic boundaries and larger than the box length with non-periodic boundaries. In the latter case, the image flags should be zero anyway, since atoms cannot be in a periodic replacted box without periodic boundaries.
The most common case for this warning is when there are bonds across periodic boundaries but all coordinates are wrapped into the principal periodic cell.
It can be legitimate for “infinite” molecular systems, e.g. a periodic graphene sheet with explicit bonds (i.e. not using a manybody potential with implicit bonds), but most of the time it is an indication of an incorrectly generated initial geometry or when turning off periodic boundaries after initially running with them and not wrapping molecules correctly (or not at all).