Chelsea boss Liam Rosenior admitted "the door is not closed" for Fernandez, despite dropping him for clashes against Port Vale and Manchester City next Sunday.
Rosenior said the Argentina star "crossed a line" with comments he made about his future at Stamford Bridge as links with him and Real Madrid grow.
With Fernandez possibly leaving west London in the upcoming transfer window, Lineker spoke to The Rest is Football podcast about how the ban was odd and is slightly unbalanced.
"I thought that was slightly odd. I don’t think he said anything particularly bad or detrimental to Chelsea. He basically just said he would like to live in Madrid.
“(Marc) Cucurella said something similar about Barcelona and didn’t get punished at all. Who wouldn’t play for Real Madrid?! I don’t understand the ban.
“Fine him if you want to punish him and keep it in-house but I don’t see how a ban helps you. It obviously didn’t make any difference against Port Vale, but I just thought it was a little bit odd."
Fernandez is now one of three Chelsea players to put their future in doubt alongside Cucurella and Moises Caicedo and the club continue to struggle despite several managerial changes.
With Fernandez contributing 12 goals and six assists this term, he will be almost impossible to replace as Madrid draw him away from the Premier League in the upcoming window.