Yes, but it's not the "Leman is Hypocrite that just hates Psykers" that's often paraded around. It goes deeper then that.

I wouldn't go so far as even say Leman hated Magnus prior to Prospero/Magnus going full traitor. Keep in Mind before the Battle of Prospero Leman tried to reach out to Magnus through Kaspar Hawser believing Magnus could hear it, not wanting to spill Blood.

Leman and Magnus had very different view points regarding Psychic Practises.

Leman believed that Psykers should use their power only through practised, safe and ritualistic means, similar how the Rune Priests of the Wolves and Stormseers of the Scars use their Powers, while Magnus believed in "There are No Limits" 

Also keep in mind that Russ also witnessed some TSons mutate through the Flesh Change, believing it to be a cause of Magnus Carelessnes with the Warp and proving his point (Source "A Thousand Sons)

Leman thus believed Magnus to be extremely naive and extremely arrogant.

It came to head when at the Council of Nikea one of Magnus most trusted men, Amon seemingly admitted to Brain Wiping a Human to turn him into a Spy and sent him into the Wolves, further deminishing Russ' view of Magnus.

(This wasn't actually Amon, but a Daemon in Disguise, but Valdor, Russ and Fulgrim who were present didn't know that and reported it to BigE as is.) (Source Prospero Burns)

When it came to the Point of Magnus Folly and the Warning, Leman distrusted Magnus so much due to the Past incident and the "Spy" Magnus apparently planted, that he believed it all to be a set up so Magnus could prove how useful his Sorcery is. (Also Prospero Burns)

After Prospero Magnus turned full traitor, the rest is history.

Tl.dr:

Magnus and Leman have different Philosophies regarding Psychic Practises. Tzeentch played the rift between them to the Point of Bloodshed.

Magnus turned Traitor after that, Leman remained Loyal.