There were 2136 inconsistent shifts. check your topology?

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GROMACS version: 2022

Dear Gromacs users,

I am studying the diffusion of water in MFI zeolite. The simulation is done without any errors. However, When I want to calculate the diffusion coefficient of water using gmx msd I see this message on the terminal screen:

there were 2136 inconsistent shifts. check your topology.

The Structure is periodic and I have applied PBC in three directions. I get a linear MSD and diffusion coefficient as output. However, my concern is that this diffusion coefficient is not reliable. What is the problem? Is there any consideration for such systems?
I also added periodic-molecule = yes to the .mdp file. But still, the inconsistent shift exists.

Thanks for your help