Usually this occurs because Shotcut was not able to detect a standard frame rate for your video and then assumes that it might be variable frame rate. Errors are common when trying to seek in variable frame rate videos because it is not possible to determine a frame position without scanning the entire file from the beginning for each frame.
Your file may or may not actually be variable frame rate. Shotcut is just warning you because the detection was not conclusive. If your file comes from a camera or smart phone, it will probably seek just fine. I have one phone that records videos that always trigger the warning in Shotcut. I just ignore it and edit the video like normal - I have been happy with the results.
My advice is to try a “test” edit with your files and see if you are happy with the results. If you export a test clip and everything plays smoothly, then it will probably work fine and you can ignore the warning.