It's not creating any problems. Its giving the IMPRESSION of problems being created because the changes in the last 2 years have relaxed the need for players to learn basic fundamentals of the game.
In seasons 1-5 there was no such thing as role selection. This meant players had to learn the game to an acceptable degree in every role if they wanted to progress. They didn't have to master a role, but they DID have to acquire a fairly complete set of knowledge about what was REQUIRED of them in that role. This meant that players in season 1-5 were far superior in terms of skill at any point on the ladder because they were more capable in more roles with more champions and this in turn lead to players acquiring basic fundamental strategic knowledge. Furthermore, because there was no role selection the ability to work as a TEAM and ORGANIZE your team and COMMUNICATE with your team to get every player on the team into an ideal situation that gave the team the best chance for success was a primary skill.
Quite simply, the reason you are under the IMPRESSION that the changes and things like auto fill cause issues in the last year and couple months is because players these days are encouraged to avoid learning basic fundamental gameplay aspects where in previous seasons the system itself FORCED players to learn these things and learn how to work as a team, together, starting in the lobby before a game ever starts, which, of course, made role selection a complete non factor. One or two people every lobby would op.gg everyone else in the lobby and identify the best possible composition with every person playing something they were not only competent at, but highly successful at, if they ever wanted to climb.
So the problem isn't that auto fill puts players who have no idea what they are doing into roles they don't comprehend, the problem is that players no longer feel a need to LEARN how to do the things they need to do in order to be successful. Which is what happens when Riot continues to dumb the game down for casual players for years on end.
In essence mate, the issue isn't auto fill, its role selection, as role selection encourages poor play habits and discourages teamwork. Things would be better if role selection was removed entirely and players were again forced to work with the team, starting in lobby, to put every player in an ideal position to contribute to the success of the team.
And just as an extra caveat, players like myself who are extremely proficient at a particular role or champ actually got that role MORE often in past season than we do with the role selection feature. People who are given a specific role are a LOT less inclined to give that role up for the good of the team to the guy with an 85% win rate in that role now then in the past. I basically got what I wanted (provided I was trying to climb and did my job communicating my effectiveness in said position) every single match in previous seasons. Every time. Without fail. People like free wins and as long as they don't feel ENTITLED to a specific role they tend to want the person with the best chance of ending the game in a win in position to end the game in a win. Role selection was actually one of the worst things to ever happen to the ladder because its become a crutch for players with a low degree of skill and talent and affords them an opportunity to avoid ever having to learn basic fundamental aspects of the game like how to "get carried" when they aren't the best player in the match.