I don't think it is a hardware problem at all. It sounds like a (known) Cura 4.1 issue. Cura 4.0 is not affected, and the issue is reportedly fixed in (the sofar not yet released) Cura 4.2.
If you have Z-Hop enabled, this could also happen mid-brim. Please try setting the Maximum Z Speed value to 5 (or so), instead of 0.
So this is most likely some kind of electronics error where the arduino in your printer (I think ender3 uses marlin and arduino) is having trouble reading the gcodes but recovers.
But to be sure you can verify that there is nothing wrong with the gcode.
Whenever you slice make sure to save the gcode "forever". I can't tell you how many times I've gone back to look at 1 day old, or 1 month old or 5 year old gcode files because I forgot what settings I had used for some part that someone later asks me about or that I asked myself about ("What the hell layer height did I use for this part again?"). Even better do "file" "save" as well which saves the project file which has even more information. I alway slice and save both gcode file and 3mf file together so I can always go back and look at what I did.
Anyway when you have a problem with a gcode file you can then take the SD card (if that's how you printed) and reverify that the file was not corrupted. You can also examine the gcode file withe cura or other methods. Cura let's you "play" back the gcode file and you can see exactly what the print head movement was for each layer.
When the printer pauses, if the ender3 shows Z position, quickly write down the Z value before you forget and then you can open the gcode in repetier host. repetier host is probably best for looking at the gcodes exactly (each line of code) and seeing where it is printing in your model. You can go through line by line and it highlights that part of your model in 3d view on the left and highlights the actual gcode on the right of the view and you can see if there is something strange in the gcode (like an M command that does a pause).
Or there could be 100 gcode moves all in 1mm of distance and that would simulate a stop. This would also be obvious in repetier host (which is free by the way).
That's what I would do.
Anyway I suspect it's a hardware problem. I had a printer that had this symptom and it really sucked to debug it. Evetually I replaced two circuit boards (one with SD card reader and one with the arduino) and that fixed it. It was very intermittent.
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