Friend purchased the new kit at the event last week at Pele Soccer, said none of the kits have the patch on, have to be purchased separately. Picture was probably a mistake by MLS or maybe they are charging more for kits with the patch already on? Something may have gotten lost in translation? I can't say why they have the patch.
Next question would be if the site has a "patch" add-on option similar to adding a name/number.
Since it's a "new" feature I wouldn't be surprised to see some changes the next few weeks to the jersey page layout/imagery used. MLS shop developers may not be up-to-date as they may just be focused on all the new jerseys on the site. I just looked on the MLS Shop site, there aren't even customization options yet, so I can't say. Even our rollover sky blue home kit doesn't have customization/player options available on the site. Probably working through logistics now in regard to patch add-ons and name/numbering.
