Problem:
Pixelmator Pro misreads the location of the mouse cursor whenever an image exceeds the Pixelmator viewport. This includes when the Tools Sidebar is overlaying part of the image. Also occurs when an image is magnified such that part of the magnified image exceeds the PIxelmator window's bounds (i.e. when scrolls bars appear).
How reproduce the bug:
Example 1 of 2: Using the Rectangular Selection tool
1. Load an image
2. Resize the pixelmator window so that part of the image is either beneath the Tools Sidebar or is beyond the bounds of the window viewport (in which case pixelmator's scroll bars will appear).
Note: You may notice the image shift vertically as this the window is resized. This shift may explain the source of the bug.
3. Select the Rectangular Selection tool and place the cursor over an easily identifiable location, such as the corner of an object in an image or the confluence of two shapes.
4. Press and hold the left mouse button to draw out a selection box, moving the mouse to the right and downwards. You should the see the bug occur at this point, with the origin of the box shifting downwards. This shift is not a snap to grid issue.
Example 2 of 2: Using the Clone tool
1. Load image
2. Resize the pixelmator window so that part of the image is either beneath the Tools Sidebar or is beyond the bounds of the window viewport (in which case pixelmator's scroll bars will appear).
Note: You may notice the image shift vertically as this the window is resized. This shift may explain the source of the bug.
3. Select the clone tool
4. Set the the source position by using option+mouse button
5. Move the mouse cursor to a specific, easily identifiable location. You should see a preview of the clone source at the cursor.
6. Press the mouse button once to place a clone of the source position at the cursor. You should see the clone appearing a short distance down the image from where the cursor was located. Again, this is not a snap to grid issue.
So, this screen grab was taken immediately before pressing the left mouse button to clone the source location:

This screen grab was taken immediately after pressing the left mouse button to clone the source location. The cursor remained in the same location throughout. Note the cloned orange dot is not at the cursor, but below it:

Edit: Also noticing the same mouse issue when using the crop tool.