about auto merge

Can you give us more details? Maybe some screenshots to see what may be going on. Most likely the merge threshold is not high enough, meaning the vertices are not occupying the same spaces and are ever so slightly away from one another.

Those vertices are too tight to have auto merge on. You should turn it off and try to clean that area dissolving some edge loops.

Also you can select those edges that have been merged already and with Control + X  delete them, then selecting two opposite vertices, join them with J to reset that whole area.

Hi Ahmed,

Auto Merge can be dangerous (I personally rarely use it), as you have experienced by now. You cannot Mask Vertices, but what you can do, is Add a Weld Modifier and use a Vertex Group that is affected by the Weld, or invert that and have a Vertex Group not be affected by the Modifier.

Maybe when Blender has A.I built in it'll tell you. Like hey Sascha, I don't know if you've noticed, Auto Merge is on, would you like me to turn it off? You're like yes please, then 10 Minutes later you see on the news a nuclear bomb was set off in your area.