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[Otorongo]

Some of my cacti are covered in these rusty spots all over them; from pinhead-sized to arbitrarily large. When I cut into the larger ones to cut them out, sometimes they go very deep; what's visible from the outside is the tip of the iceberg.

This is affecting my pachanois, but not the bridgesii or peruvianus.
I've also spotted those on my L. wiliamsii.

What is it and how do I treat it? I have a systemic fungicide (for roses), would that work?
I remember seeing these rusty spots years ago, at my previous place and can't remember how it ended. Will they eat my collection, or will the warming weather strengthen the plants enough so they can fight it on their own?

[Greenmystery]

Are they all in the same mix??
Not perhaps too moist at the roots

[Otorongo]

Are they all in the same mix??
Not perhaps too moist at the roots

They're in the ground. The natural soil here is clay and it was amended before planting. It may be too moist at the roots.

It's getting warmer and drier though, will that heal my cacti?

[Mangrove]

May you please post more pictures of what you are describing? When I was living in GNV Cacti would die on me left and right. I may or may not have had this problem before, and given the sad history of the innumerable trichs I lost to maladies up there I would recommend you take cuttings at least a couple inches above wherever you're seeing these rusty blemishes at just in case.

[triplenipple]

I would say it's either the start of some rot or possibly sun scald.  If rot, push on it and see if is soft to the touch.  Rot that I've seen on my cactus can start this color and then turn black (possibly oozing) and goes systemic.  Sun scald starts as a rust and turns into bleached dry area.  Scald isn't that much of an issues other than visual appeal from my experience.  Post some more pics and let us know if things start getting worse. 

[ONandONandON]

i would guess to much water