I can think of one example that I've seen a very long time ago for this type of inconsistency, and which I'll occasionally use myself: "0.1uF" means it's a bypass cap, "100nF" means that it's anything else. I'm not at all saying that this is why it's this way here, just that it's just one reason that I've seen it done.
When there are a lot of ICs on a board communicating using SPI or I2C, mixed in with all sorts of comparators and op-amps, you're going to have a ton of small capacitors, half of them probably bypass caps. To make the schematic a bit easier to read, I'd put "0.1uF" for all of the bypass caps, because that's an explicit exception to how I'd normally write that value -- "100nF". That way when I come back to that schematic a couple of years later and try to figure out why everything is laid out the way it is, I can "ignore" the bypass caps. Anyone else looking at the schematic might be annoyed at the inconsistency, but it won't interfere with them reading it.
But that's just me.