I have encountered these problems as well. In several cases (different locations, dates, hotels) the lowest price was not available for any room type considering taxes and fees. It must be the "lowest price ever available" at this hotel for the broom closet
I had cases were SOME taxes were included, others not.
I do think these are IT problems - a mixture of design and execution mistakes, resulting in sometimes different prices (with/without taxes) being displayed and sometimes inaccurate ones. This has been going on for a while, so I don't think anybody at Accor is giving this a lot of attention.