Just did a test on ArcGIS 10.3 with 3 featureclasses in a File Geodatabase and it worked for me:
Do you have more details (what data sources you tried, which columns you selected, are the featureclasses used by other open map documents, etc)
2019 and still encountering this problem. I need to use the Delete Field (Data Management) tool to delete several dozen fields from a large feature layer. (in this most recent case, 43 fields in a feature layer with 105,533 features). I've tried this workflow in ArcMap and ArcPro on multiple data sets, and in both situations it caused issues. The data set ends up getting corrupted and it often crashes the software as well.
If I go through and delete the fields one at a time, it's usually fine. But the whole point of the Delete Field tool (rather than just right-clicking a column in the attribute table and selecting "delete") is to be able to do multiple fields at once...I would think it should be able to handle this. Are there any ideas as to what could be causing this?
Thanks for any input.
Update for anyone who may encounter a similar issue:
I spoke with Esri Support and we tried a couple of different things. Ultimately, the workaround we found that suited my workflow needs was to use the Feature Class to Feature Class tool. When using that tool, I deleted the fields I didn't need from the Field Map menu. This created a new feature class in my established geodatabase with only the fields I needed while maintaining my field aliases and domains (this was critical the data will be used in ArcGIS Online and needs to have standard formatting).
This was done in ArcMap 10.6.