I am using QGIS 2.8.3 but also have 3.4 whatever works better for this issue.
I have a bathymetry shapefile and a point layer. One of the columns of the bathymetry vector gives the maximum depth and I display the file by the different depth classes. Now I need to know how many of my points (point layer) are in which depth class. I tried to use the 'points in polygon tool' but it did not work, maybe cause there was no way to indicate which is the relevant column (depth max) cause the attribute table contains quite many columns.