Q:

Select By location QGIS 3.12 Not Selecting all Features within

I'm using QGIS 3.12, trying to do a simple select by location between two polygon layers. 
However, once complete it never brings back correct results (does not select all polygons within selected layer). It either selects too many, or not all polygons that fall within boundary (red line).
I have tried multiple different choices (intersect, contain, and both selected together)... never getting it to work. 

A:

When I'm faced with situations such as yours, I first check my data.  I would start with the following checks:

Both layers, red and black must be in the same coordinate reference system.  Confirm the CRS for each layer by opening its layer properties and selecting the information tab, then look at the CRS.  If the CRS values differ, you must project one or both so that they have the same CRS.
One or both layers may have geometry errors.  Use the Vector > Check Geometries tools, and if errors are reported, correct them.
The red and black boundaries may not align exactly at a microscopic scale.  That is, they may appear to align on-screen when zoomed out, but if you were to zoom in far enough, you might seen that the red and black lines are not spatially coincident. In that case, Select by Location is doing its job correctly.

