Brown markings.

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@Lance: not surface stains. Mee to I know this problem. Its bacterial. I treat it with Physan.
It seems to me that this plant should be repotted.
 
If you can't wipe it off, just leave it and separate it from the rest of your plants. Spray it with the fungicide that is recommended for orchids...your choice I don't want to recommend chemicals.

I don't think it is a bacterial problem, otherwise, you would have lost the plant a long time ago.
 
I have seen this from time to time on phrags back when I grew on the windowsill. It is not rot and to my recollection has no bearing on anything; I have always ignored it. Will wait for the phrag experts who might be able to give you a better answer. Have not seen it in the greenhouse lately.
 
I had similar markings from adding pro-biotics to my watering solution. I did rinse off right away but could totally see that stuff staining if allowed to dry. Even the roots browned (not the normal fuzzy khaki color) for a little while.
 
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