There are too many painful points to list them all. If you absolutely insist that the player need to do it manually, then at least give each skill its own dedicated training spot.
I will list four examples.
First the menar tree that you can't cut down. This is good because you can just spam the action key. There's no unnecessary dialogue. You don't stop training until you want to.
Second the crystal ball in the reliquary. It has two options, mana control and starsight. You can't spam the action button if you want to do starsight because it defaults to mana control. So you have to navigate the menu and push enter each time. Which takes longer even if you do it right, and if you do it wrong, well that's a wasted action.
Third reading the books in the office. You select the book from the list, and then it takes you to a continue or leave menu instead of back to the full book list. This lets you spam the action button. This is much better. If you're going to have spots that can train more than one thing do it like this please.
Fourth woodworking with menar wood. Mr. Harris exclaims "Where did you get that!" and then pauses every single time before it gets to the menu to actually do something. There is admittedly not a lot of menar wood so you can't really spam it. But you can still do it several times in a loop so it gets annoying. It's also weird. Why is he questioning me about Menar wood when he literally just said that. Maybe only have him do it the first time each loop.
In summary, I don't mind the grind so much as all the unnecessary button presses and waiting. Lets us just mash the action key if we want to train something. Training the different magic things is also painful because even though you can just hit the action button it has several lines of dialogue each time.