There are a number of different error messages you might see on your Ultimaker 3 or Ultimaker 3 Extended regarding the active leveling process. There are a few different errors you may see, but the most common is "Difference between detected height of both PrintCores exceeds realistic values."
Your printer always expects to find a height difference of 1.5mm between your left hand (Slot 1) Print Core and your right hand (Slot 2) Print Core. The left hand Print Core is stationary and will always be at the same height. The right hand Print Core moves up and down 3mm depending on the position of the Lifting Switch on the right side of the printhead. This allows it to always be either 1.5mm below the left hand Print Core, or 1.5mm above the left hand Print Core. When the Print Core in Slot 2 is actively printing, it will be in the lower position, so that the Slot 1 Print Core does not drag over the printed parts. When the Print Core in Slot 1 is actively printing, the Print Core in Slot 2 will retract out of the way.
If there is debris on your bed, or filament hanging off the end of your nozzle, it will change the perceived height of the bed. It's not uncommon for filament to appear on the tip of the nozzle during the active leveling process, because the Print Cores do heat partially during the active leveling. If this happens, wipe the Print Core off with a paper towel, and try the active leveling process again.
One of the other most common reasons to receive this message, is usually that the build plate is starting from too high of a position at the start of the active leveling process. When this happens, you may also see the nozzle of your Print Core get pushed inside the print head.
Compare these photos:
In this photo, the bed is too high, because the spring tension is too loose. You can see quite a larger gap between the bottom of the heated bed plate, and the tallest part of the metal lip on the base plate. You can also see that the right hand Print Core has been pushed up inside the nozzle to the point where it is now at the same height as the left hand Print Core. The 2 Cores should never bee at the same height.
In this photo, you can see that there is only a very small gap between the bottom of the heated plate, and the tallest part of the base plate's lip. This is because the bed springs are correctly tightened. You can also see that the Slot 2 Print Core is hanging down lower than the Slot 1 Print Core; because the bed is at the right height, the Core has not been forced inside the print head.
This video will walk you through tightening the thumbscrews and spring tension to resolve this error.
Another way to check the height of your bed is to print this 14mm spacer. In a pinch, you could disable active leveling, do a manual bed leveling, and print this, and then go ahead and turn your manual leveling back on after you've checked the height.