I have encountered the same problem. I think it works this way: If you delete a mastery page during champion select (new draft pick, don't know if it apllies to blind pick as well) you will still be shown the mastery pages you had when you entered champ select. However if you pick one, you will play with whatever page is now on its place.
For example, if you have 5 pages
1 Top
2 Jungle
3 Mid
4 ADC
5 Supp
and you delete Mid, it will still occur in the drop down menu. If you then pick ADC, which is the 4th in the drop down menu, you will actually play with Supp, because it is now the 4th.