It's important to make sure the XY calibration is accurately aligned. Every Cores is unique; it has a serial number embedded in its firmware so that the XY calibration you've done previously will always be remembered, even if you remove the Core from the printhead.
Your Ultimaker 3 series printer ships from our facility in Memphis with 3 Cores; a .4 AA Core should arrive in position 1 in your Printhead. A second .4 AA Core and your .4 BB Core come in your accessory box.
Every pair of Cores in each printhead has it's own XY offset. The three Cores that have shipped with your printer are calibrated in 2 ways; the Core in position 1 has been calibrated with your second .4 AA Core in slot 2, for printing with 2 build materials (like PLA and PLA). The Core in position 1 has also been calibrated with your .4 BB Core, so you can print build material and PVA. Each printer permanently the XY offset calibrations of the Cores you've installed in it.
However, if you switch the left and right positions for a pair of Cores, install a new Core in one of the positions, or put your Cores in another printer, the printer will prompt you to run the calibration again. If you've misplaced your XY calibration sheet, you can download a new copy. Follow these instructions for performing the XY calibration.
If you've recently performed an XY calibration and find that your print doesn't seem to be lining up right, go ahead and re-run the XY calibration again, looking closely for where the lines match up perfectly. For example, on this print, the attempt on the left was made with uncalibrated Print Cores, and the PVA printed on top of the PLA where it should have been next to it. This print would have failed. The print on the right was done after the Print Cores had been calibrated, and finished successfully.