It is said that the Ionian (major), Aeolian (natural minor), and Locrian modes weren't really three of the ancient church (Gregorian) modes. What is the reason?
Historically, the modes were methods of classifying chants. There were few if any chants having the note patterns that fit the Ionian or Aeolian or Locrian modes. Later (1400s or so) Locran wasn't used as the natural fifth above the final note (B) was diminished. Actually, in the earliest known chant descriptions, the note B was mutable (B soft written "B" being Bb and B hard written "H" being B natural; this practice has been followed in German writings.) (Other languages may have written them differently; some used B-moll and B-dur or the like.)
The modes roughly described the range of chant melodies. From D to d (an octave with scale steps D-E-F-G-A-G-B-C-D with half steps between E and F and between B and C) was the normal Dorian; lower would have been A-B-C-D-E-F-G-A (called Hypodorian meaning below Dorian) to describe chants that had a different range. The final note in both cases was a D. (The pitches were relative, not absolute.) This would have been the Aeolan were the chants to end on A but most ended on D in this classification. Similarly for Hypolydian (C-D-E-F-G-A-B-C) with F being final and Hypophrygian being B-C-D-E-F-G-A-B. The scale patterns existed but were not considered separate as the chants didn't end on these notes.
Hypomixolydian had the same pattern as Dorian but with different endings.
During this time, the hexachord classification was also developing and used along with the modes. The "soft hexachord" F-A-Bb-C-D-E, the "hard hexachord" G-A-B-C-D-E, and the "natural hexachord" C-D-E-F-G-A-B. These were written in an overlapping manner and allowed one to describe "modulation" between modes. It was very complicated. Check Google and the Wikis about chant modes and hexachords.
Later in the 1500s some authors did allow for 12 modes and some for 14. With the invention of F# and Eb then C#, etc., things got more complicated until by the 1800s, the current naming became common.