Your stimulus position exceeds the X or Y window dimensions. Stimuli centered beyond the window will not be completely visible.
This issue is often caused by an inconsistency between the units of your stimulus and the values being requested. For instance a position of (3, 0), when the units are deg is sensible (3 degrees to the right of the screen center) but a position of (3, 0) when the units are height would not be sensible (3 times the height of the screen to the right of the center).
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Check the position and the units of the stimulus carefully. You may also need to check the monitor calibration if you’re using units that depend on the monitor size and resolution (like cm and deg).