Upstairs bathroom: sounded like it was still flushing(water running) went upstairs and no one was in there so I went to flush it but notice water was dirty in the bowl thinking it was my kids I flushed it and it flushed but dirty water still ended up in the bowl... so I looked in tank and there was dirty dark brownish water in there as well so I flushed again while looking in the tank and no change still dirty in the bowl and tank...

Downstairs bathroom: after seeing what had happened to the upstairs bathroom I checked downstairs and water in bowl was clear so I flushed juss to see if it would end up like the upstairs bathroom and sure enough it started to get dirty! Can someone help and let me know what is going on Please!

Is the water Ok in other places?

If the water is OK in othere sinks/shower then the problem is with your toilet supply line or the fill valve.

Close the angle valve under the toilet tank remove the cap from the fill valve hold your hand on top of the fill valve turn on the water to flush out all the dirt out of the fill valve see if the water is clear now if not come back and will tell you step by step to resovel your issue, also please see the images below and tell us which fill valve do you have, Thanks.

John

You may be seeing rust deposits that were stirred up in the tank by the water running so long. Keep flushing it out and it should clear. I have the same issue with 1 toilet and not others.