Dies were sometimes cut on a piece of diestock that was a larger diameter capable of accommodating the design for a bigger denomination. We know that die faces were ground down once deemed sufficiently degraded and a new die engraved on the end of the bar. That new die may or may not have been the same denomination as previous. In the case of the Oxford 1645 reverse 7 above, the two diagonal flaws on the bottom line below the declaration along with the cluster of dots in the centre are quite likely to be the remains of its previous incarnation where the detail wasn't fully ground away.
As to why they got the diameter wrong, I think it is a case of die worn out/broken, so quickly recut a new one and get production going again. The quality of the detail on many of the known dies has all the hallmarks of hurried work. You do get the occasional one where more care has clearly been taken, but the overriding reason they were making Royalist issues was for the immediate payment of troops who would almost certainly be there for a limited time only, so speed was of the essence. You only have to look at a significant proportion of yesterday's coins to see the crude polishing lines on many dies that tell you they we made in hurried circumstances. So, in summary, I would think the reason the size was wrong is down to the fact that they would be more interested in getting production going than looking for precision in the design. It is particularly obvious on some Shrewsbury shillings, where the 3 line declaration clearly shows a shilling was the intended denomination, but the die is hopelessly oversized. See scan below where the obverse is full, but the reverse is significantly short.
I wrote an article on the Chester halfcrowns to this effect and also the identification of a faulty rocker press in the final Circular of January 2014 where I could show that the CHST below obverse die was recut to make the Declaration issue obverse. The important observation was that the die was recut with the new detail significantly offset from the position of the previous to the extent that the only rational explanation was a die face suitable for a larger diameter. Coincidentally it also gave an immediate explanation for why the Declaration reverse die broke from the offset or very soon after.