I had a series of errors recently while I was trying to run a few geoprocessing tools manually on layers within a group layer. The error message kept saying it couldn’t open the layer, even though the layer was clearly in the map. Even restarting ArcMap did not help.
I eventually discovered that geoprocessing tools may randomly fail on layers which are part of a group layer. I say randomly because sometimes the tools would run as expected, other times not. I’ve only experienced this anomaly when using the ArcMap interface – running the same sequence of tools on all the layers in a group layer in a for loop in Python does not give this error.
Everything is Spatial 
Sometimes turning off the Background processing in Geoprocessing options helps.
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I’ve had it off since upgrading to 10.3 since I don’t really run tools through ArcMap anymore anyway, so I prefer them to stay in the foreground if I do. It doesn’t help 😥 Now I just don’t run tools manually on layers in groups anymore 🙂
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Having the same trouble here, using ArcMap 10.3. Can’t figure out the rhyme or reason. I can usually drag the layer out of the group and it will work fine. Frustrating.
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