I think this should help:
/clear @p minecraft:name_tag{HideFlags:4,display:{Lore:["Used at a gate twice."],Name:"{\"text\":\"Train Ticket\"}"}} (this will remove all the tickets from the nearest player)
or
/clear @p minecraft:name_tag{HideFlags:4,display:{Lore:["Used at a gate twice."],Name:"{\"text\":\"Train Ticket\"}"}} 1 (this will remove 1 ticket from the nearest player)
or
/clear @p minecraft:name_tag{HideFlags:4,display:{Lore:["Used at a gate twice."],Name:"{\"text\":\"Train Ticket\"}"}} 2 (this will remove 2 tickets from the nearest player)