From the comments - you used a different brand of whole wheat flour this time around. My best guess (and really that's all anyone can do with something like this as there are way too many factors) is that this new brand is the reason for the difference in the bread.
Just because they are the same type of flour, it doesn't mean they are all milled, sieved etc. the same way.
It may be this new flour is:
- More coarse or finely ground
- Different additives
- More of the wheat husks are sieved out
All these factors can effect how the bread cooks as well as how much liquid the flour absorbs.
I would say it is very unlikely that your bread machine has broken since it sounds like the bread still cooked!
It's also unlikely that the bread will cause you any harm. An enriched plain loaf bread mix can be eaten raw (not that you'd want to).
Please feel free to edit my list with any other changes flour can have between brands.