Was it a misprint?
It appears that the minimum number of trains required to complete a destination ticket was only the starting point for assigning each ticket a point value. The claim is made (in this post by Days of Wonder Forums user "Caboose") that Alan Moon (the game's designer) said the ticket values were not supposed to be the shortest route between two cities. Lacking the context that this may have been said in, I believe the intent was to put to rest worries that some ticket values were mistakes or misprints, rather than to deny all connection between tickets' values and their minimum lengths. (This post by Caboose from several years earlier shows (s)he had previously believed the issue was due to a misprint.)
Additionally, if the changes made in the 1910 expansion were to "fix" the tickets to match their minimum lengths, they didn't fix all of them. It's been pointed out (in this post by Days of Wonder Forums user "DiscJet") that the Los Angeles to Chicago ticket and the 1910 expansion's Las Vegas to Miami ticket are each worth more than their shortest length.
Most likely, Mr. Moon increased values for certain tickets to give a slight additional incentive to choose them (especially given the different mix of tickets that would be used in 1910). Was it to balance out a disadvantage of these tickets, or to slightly change gameplay with a small advantage to certain routes? I wouldn't have a clue. However, I doubt it was a misprint.
How should custom tickets be valued?
The majority of tickets should be valued at the minimum number of trains required to complete them. Then think through what your goal is for adding those tickets. Do you want to create more competition for certain cities? encourage more cross-country routes? discourage the use of 5- and 6-train sections? Once you've clarified that goal, you might adjust a few custom tickets' value up by one point (maybe two) based on play-testing or your anticipation of the results.
In general, adding a small number of destination tickets, even with tweaked
values, isn't going to have a very large effect. If you've played with the Mystery Train routes (but still without the other cards available in the 1910 expansion), that would probably give you a good idea of how much of an effect your changes would have on the game.
Attribution Note: The first section is partially an adaptation from my answer to the question "TTR: Destination ticket value changes in the America 1910 expansion". I don't have access to my copy of Ticket to Ride and the 1910 expansion at the moment, so I can't verify the route lengths or values myself.