I had the same error message when running a Python script containing an Intersect and then a SpatialJoin. I enabled Background Processing in the Geoprocessing Options (no idea why it was off) and suddenly it worked.
Thanks tojthompson88 - in my case at least it was fixed by change the way things were named in the Table of Contents (ToC). Specifically, the layers that were failing were in a Group -- with a space in the name. ArcGIS 10.3.1 with 64-bit background geoprocessing on. I use underscores EVERYWHERE but the ToC. Now including the ToC.
Be careful there are no lock files on the layer. Sounds like an access issue to me.
Tip 1: Don't use shapefiles. File GDB featureclasses are much more reliable and consistent when it comes to editing.
Tip 2: When getting an additional warning that the number of records don't match the number of rows, make a backup copy of the shapefile. Then delete all of the file extensions for the shapfile except the shp, dbf, shx. Copy the dbf to another directory and then add it to a blank ArcMap where you can edit it. Hopefully it will be obvious which records should be deleted. Typically these will be exact duplicates. Delete them both. Then go back to the copy where the shp is and rename the dbf to "<name>_old" then replace with the edited dbf file.
Worked great for me!
Same frustrating problem here. Anything tryied. No fix founded
Please see this as a possible solution
I was having this issue running the Append tool in ArcMap on a feature located in a feature dataset. I ran the tool in ArcCatalog and it worked.