Given it is MRI scans, I strongly suspect this is a rounding error in the originating Philips DICOM dataset. It is unfortunate, but the use of ASCII text with only a few decimal places make rounding errors common when images are acquired with a rotation relative to the scanner bore. In this case, dcm2niix faithfully reports that values reported by the DICOM header, and there is no perfect way to store this as a QForm. If I am correct, this reflects a limitation of the DICOM format, and Philips use of very low precision for the spatial coordinates. Since the warning does not reveal the magnitude of the error, you may want to visually inspect the data to ensure all is well. You may also want to contact your Philips research collaboration manager and lobby them to store spatial coordinates with more precision. In practice, with the subsequent non-linear normalization I doubt these tiny rounding errors have any influence, as the registration algorithms will find the same minima regardless of tiny difference in starting estimates.

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