I thought it might be useful to say what an institution is. Google tells me they're structures or mechanisms of social order, and govern the behaviour of a set of individuals within a given community. Institutions are identified with a social purpose, transcending individuals and intentions by mediating the rules that govern living behaviour. A slightly broader definition is an established organization, a place where an organization takes care of people for a usually long period of time, or a custom, practice, or law that is accepted and used by many people.
Hopefully we're at least on the same track - a broader rather stricter definition. My thinking about institutions has only crystallised after I recognised the way I was reacting to them in life.
The first major institution I reacted to was school when our children were faced with it. In hindsight I struggled with the main purpose of schools (education) and other purposes of schools becoming more important. These range from baby-sitting (to allow parents to work) to producing citizens who accept things promulgated by "authority" (rather than think for themselves). Of course when people reject "authority" simply as an act of rebellion that brings different problems.
Next was business. Having worked for the government and found the internal politics too frustrating, I worked for a few smaller firms. They were good - but often ended for less than brilliant reasons. A couple ended because of mismatches between me and the role, which was sad - and others ended because of takeovers. My last employment was the best - primarily because of the CEO. When I asked for something, he'd say "yes", "no" or "see me in the morning" (when he'd then say yes or no). I didn't appreciate the negative answers - but he was the boss.
I eventually I left that job to go into public practice as a chartered accountant, where I could be closer to the decision makers. We'd been taken over by a firm ten times our size. The difference this time was the takeover was so my boss could become CEO of the larger firm. It was a bit of a shock to them - and to him - but my personal move came when I realised internal politics had taken over and my boss was no longer able to function as he had previously.
Church is another institution that had me baffled for a while. I still think the way Jesus set before his followers is the way to God. I now see that Constantine in the 3rd century turned Christianity into a religion that distracts it's followers from God. That's not to say believers are on a path away from God - just they are often hindered in their walk with God by things religion promotes. I won't go into these now - there's plenty of information elsewhere. But the way Jesus founded never had buildings, paid staff or almost anything we think of today as "church".
There are other examples of institutions - but these are three I have had some experience with. I'm not putting down specific institutions - the reason they become institutions is wide-spread acceptance of the basic function they perform. But all too often the institution eventually takes primacy over the goals that gave rise to them. "Heretics" break away from the masses - think of John Holt in education, Richard Branson in business, and Frank Viola in church.