Having the alignment marks off slightly should not make a difference, or, at most, a very small difference. It's my understanding that the marks were more important in earlier days as a way of tuning out wedge and astigmatism, but that is second or third-hand information and should be treated as such.
it probably did not happen during shipping, but may have resulted from someone messing around with the lenses or cleaning them in the past.
in my experience, people who ship refractors another optics incorrectly are generally not the most reliable people to have dealt with, and may have abused or been careless with those scopes while in their possession. Harsh, but there it is. And I've been fortunate enough to be able to research and correct some of these messes that came into my possession. Almost always undisclosed.
Which raises a possibility, in the event there is an actual problem.
You sound unhappy, so I'll take a flyer with one suggestion, since it's happened to me twice now.
I've had two refractors with a reversed element, and one with a completely reversed cell. My memories on the specific if shoes are faint, but I seem to recall an increase in spherical aberration in possibly chromatism. Possibly field curvature as well, but that may have been the reversed cell, not the reversed single element.
If the edge marks were not arrows, but simple lines as is most common, an element, likely the front, could have been flipped. The rear is usually a convex concave Flint, I assume your lens is a contact or air spaced fraunhofer achromat.
I researched optical prescriptions back then to resolve what I thought was a flipped element. My recollection, and only a recollection at this time, is that fraunhofer achromats have identical or almost identical curves on the two innermost surfaces. Assembled, with thin spacers or in contact, Newton's rings should be visible, more so with monochromatic light such as a green filter over a fluorescent bulb or a diffused laser from a collimator. I used a green laser pointer. But the 'lenses kind of stuck together by suction' test works just as well for identical curves.
I first estimated the curve by measuring the height of the edge when the lens was balanced face down on a pec pec on a table IIRC. The Baker achromat had a very large spacer, but again, the curves were nearly identical so I simply put them in contact with one another and the different curvatures of the two sides of the front element were immediately obvious.
The correct, matching, curves matched so closely the lack of air space made them almost want to stay together.
But, of course, a warning.
It may be nothing wrong with your lens, or nothing wrong, at least, with its assembly.
I've hit enough of them, that I wonder how many SCTs with misrotated alignments, and refractors with flipped elements, are out there, almost certainly the result of cleaning that probably wasn't necessary, and was done without care to maintain the original alignments and orientations of the elements. I guess I'll have to mention overtightened retainers damaging flints on older lenses, or simply causing astigmatism by mechanical stress.
I make sure I mark all possible points of alignment, as well as sky and eyepiece side, if I'm forced to clean something. but usually, I grit my teeth and tell myself 'don't even think about cleaning it'.