I have been running into a bug with my QGIS 2.16.3 project. It has to do with editing a shapefile after closing the QGIS project and restarting the computer.
So I have a spreadsheet of locations of interest that I plot on my map. I complete this activity by first converting my spreadsheet to a CSV file then adding a new Delimited Text Layer to my project. My spreadsheet has a column for X and Y coordinates so I assign them to the correct field in the "Geometry definition" section. The data points show up in the correct place in my map. After this, I would like this file to be a shapefile so I "Save As" the layer as a shapefile and I am now able to edit the attributes in the file. Everything is fine until I close the project and QGIS program.
When I open the QGIS project up again, my newly created shapefile is still a shapefile, however I have lost the ability to edit the layer. My traditional way around this would to "Save As" it again as a shapefile and I would regain the ability to edit. However, this means I have to copy over all the rules, filters, and layer attributes I assigned to this layer.