Without going back and double checking, I sort of remember the same thing happening with us. I remember researching it a bit and finding that in the case of our standardized testing -- Language was the phonics category. My child still isn't great at phonics.
But she reads well and scores high on comprehension -- 90% - 99% depending on the day. Spelling, however, was never (and still isn't) a strong skill. This is probably a result of that low language score. I worked a little with her, but decided to not really fret over it. As I recall, they quit testing phonics after 4th grade. And if her reading comprehension is fine and the spelling is mostly okay... I decided not to worry about it.
