Using the CTRL/COMMAND-L feature is a great and quick way to place objects, sadly the model does have some "bumps" at the bottom. So depending on what face you select to place on the bed the model might even be rotated by a few degrees.
Looking at the model it looks like it's been smoothed inside MeshMixer. Things like this happen when people get too close to the edge of a model
when smoothing.
Another way of fixing this is by using a free tool (like MeshMixer*) and use it's "Plane Cut" feature. But a small move along -Z often is enough, great you got it working
*Some slicers also have a plane cut feature. And some won't even allow moving an object freely along Z, so it's always a good idea to get used
to a small tool for small fixes like this