It's always disappointing when something like this happens and I do sympathise with you. I experienced the same problem 16 years ago with X. borealis tadpoles. I cannot honestly remember what the eventual outcome was but I seem to think that some of the froglets had twisted spines. I bred the frogs again 8 years later expecting the same thing but on that occasion the problem I encountered was tadpoles with deformed forelimbs resembling "spindly leg syndrome" that breeders of poison dart frogs sometimes experience with their froglets.
I don't know what the cause is but I suspect that it might be related to a mineral deficiency in the water as I live in an area where the tap water is very soft (ie: low in Calcium and Magnesium). Below is a link to a paper about water hardness (GH), which concludes with "The common features of all the water sources evaluated that resulted in high survival and normal development of Xenopus embryos are a high concentration of calcium and a high GH value. Thus, we conclude that water hardness should be an important consideration in housing Xenopus females to be used for oocyte production." The article's a PDF document at: http://www.xenopus.com/Water_Hardness_final_proofs.pdf