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What could have caused this and should I lop it off?

It is a little thing in a 3" pot, and I believe may be an Echinocereus morricalii?

Looks like it has not got enough light and has suffered etiolation. Yes does look like an echinocereus morricalli.

Thanks ade.

Even though I withheld water during the winter, did I not keep it dark enough and am I stuck with that nub?

With Echinocereus, you can cut the tip and it will probably send out new stems from the damaged area. Here's an example.

Its probably the dark that did it, I keep my plants in as much light as possible all year round even when hibernating. The echinocereus are quite a hardy genre so will grown at cooler temperatures so the growth period can be later in winter and earlier in spring than some others. I do rest my plants with approximately 6 months of dry but always give the maximum amount of light possible. You may have put it in the dark a little early or brought it out a little late which cause the stretched out growth. While cacti are hibernating they can take darkness as they essentially are not growing but knowing when they have stopped growth or started can be tricky best option would be exposure to as much light as possible and stop watering, they will slow down and then hibernate with out risk of etiolation if they are still actively growing. In the wild the hibernation period would be for most during the hottest parts of the year its really an compensatory option hibernating in the winter giving the plant it rest during the period of difficult cultivation.

Thanks!

"As much light as possible" during the day, that is - they generally need long nights during Winter dormancy, and cooler temperatures. Some species may undergo heat dormancy, too, but for the most part they grow in regions where Winter is the dry season, and that's their main dormant period. This species is native to northeast Mexico.