When importing several layers with importer for which CRS identification failed (typical of Shapefiles) a CRS entry tool will appear for each layer including a text entry and a 'Find' button. If the find button is used to look up a CRS, it will fill in the the text entry. Whether the CRS was typed or 'found' a button at the end of the line for the layer allows it to be "applied". If this is done, all other unapplied CRSes that were entered using 'find' will be cleared. Those typed in manually will remain.
To replicate, import a directory of 2+ shapefiles. Enter CRSes for two of them using 'Find'. 'Apply' one and the other will be cleared.