Colombian Bernal cracked in the 15th stage on Sunday, losing eight minutes on the leaders, before the 23-year-old withdrew ahead of Wednesday's 17th stage because of back pain.
Four-times Tour winner Chris Froome, 35, and 2018 champion Geraint Thomas, 34 were both left off the Ineos team this year due to lack of form.
"It just shows you... all isn't well in that team... They backed Bernal because he's their youngest asset and there's a longevity there," Wiggins, the 2012 Tour winner, said on Eurosport's The Bradley Wiggins Show https://www.podbean.com/podcast-detail/jddmm-6fc2a/The-Bradley-Wiggins-Show-by-Eurosport-Podcast.
"The others, age isn't on there side and it just shows how cut-throat it is, if you can get rid of a four-times winner of the Tour, a British born and bred product of that system in Geraint who's a flagship for that team or what it was.
"... They've pulled him (Bernal) out too late... because they're looking after his welfare but clearly his back isn't well, his knee's done and they knew that before the Dauphine so it shows you just how invested in his future they are there."
Froome, who said his old boss Brailsford would be facing the sack if he were a soccer manager, added there were "too many chiefs" in the team.
Wiggins also had sympathy for Giro d'Italia champion Richard Carapaz, who was called into the side for the Tour.
"Carapaz...? He was looking forward to the Giro and would've been in good form for it, but G (Thomas) has got the Giro, so the defending champion of the Giro is now riding up the road trying to win a stage of the Tour," Wiggins added.
"Froome, they've given him the Vuelta a Espana, last pickings as it were, but now Bernal might be doing that, so what happens to Froome? They've got too many chiefs there." (Reporting by Shrivathsa Sridhar in Bengaluru Editing by Christian Radnedge)