In thin sections, I see reddish brown patches or stains in the magnetite? I think it's like an alteration of magnetite....so what is this reddish brown mineral?
a general iron oxide transformation pathway, starting on magnetite would involve the following fundamental steps, in mafic systems: magnetite >maghemite > hematite.
So, the reddish brown patches which you see could be hematite.
However, it could be useful to know the rock-type as well as to see some thin section pictures.
Magnetite commonly alters to hematite or goethite. Most likely this is what you are observing. If you examine the section under reflected light- hematite should have a higher reflection than the magnetite, whereas the goethite is lower. This is how you an distinguish them. Hematite can also occur as exsolution lamellae or lenses in magnetite. So it also depends what your are examining- a primary or secondary mineral.