EMR warning when meshing? 3D

Glad to hear that you found the reason.

Thanks for the in-depth answer Faseel.

Good to hear about the tabulate command in the Mesh mode, which I have not been fully utilising - thanks for that.

The problem was due to one level of surfaces/volumes being too closely spaced to the soil strata (Ctrl+L), hence why I could not anticipate this with checkgeometry only.

This message means that the Enhanced mesh refinement (EMR) feature is finding some small surfaces after intersections and also small edges which could also be the result of intersections. 

It would be a good practice to always first check the geometry using the command line by typing in certain commands or by clicking the check geometry icon in the middle tab found in the Structures or Mesh modes. 
You can find close proximity issues in the geometry by using this command in Structures and Mesh mode:

checkgeometry

This command checks if objects overlap or are adjacent and gives a list of items with their distance. So please check here the geometry that is marked as being close by.

In some cases, this command does not give any feedback. This command by default takes a distance tolerance related to the model's size. If the command does not give this info, then add a parameter to this command, e.g. 0.01 to check all geometry that is located within 0.01 m:

checkgeometry 0.01

You can also check the size of the of the intersected objects in Mesh mode to locate problems. To do so, make use of the tabulate command, see the examples below. You might want to adjust the numbers below to fit your model's size.

#To find small Surfaces:
 tabulate Surfaces "Area" "Area<0.5"

#To find small Polycurves (e.g. used for Tunnels):
 tabulate Polycurves "Length" "Length<0.1"

#To find small Volumes:
 tabulate Volumes "Volume" "Volume<1"

#To find small SoilVolumes:
 tabulate SoilVolumes "Volume" "Volume<1"

The list of Volumes might be different from SoilVolumes if you model volumes outside the borehole soil layers.

More details on the tabulate command, see here:
https://communities.bentley.com/products/geotechnical1/w/wiki/45942/obtaining-tabulated-data-from-plaxis-input

Apart from that, the snap and mergeequivalents commands can also help in making the geometry accurate in order to proceed in meshing procedure. For more information about these commands please check our Reference manual and Command reference (Help menu).

Please try to locate all potential problematic geometry in your model in Input and fix them. Note that not all reported objects are necessarily problems that need to be fixed.