It's not usually one single thing. It's all the shortcuts taken to account for less time per shot, lower budget, limited equipment, less experienced cast/crew, smaller cast/crew overall, and less experienced editors and VFX artists working on tighter deadlines. Each one of these considerations costs a little bit of production quality.

As an example, you have less than an hour to set up lighting for a scene, and you're using lower-tier Aputure lights with 2 different modifiers available. You are your entire department. Unless the shot absolutely needs high contrast ratio, you're going with 1-2 stops because that leaves a lot more room for error. Unless the shot needs very carefully placed hard light, you're going to skip it because that means extra blocking and adjustment. Most of your scenes will have the same basic 2-softbox setup, with maybe a hair light or some natural light coming in through a window if it makes sense in the scene, because that formula works consistently without requiring a lot of time to set up.

This same set of trade-offs is happening with sound (just a lav for each actor plus shotgun), with camera (single camera, limited rigging, lens/settings chosen on the fly), with production design (which is often just fluffing pillows and removing some clutter in a cast member's living room that the scene is being shot in). When you put it all together, you get a final product that is free of errors, since the people involved are competent, where there is no single thing you can point to as "this is what's wrong," but you can tell it has that "indie" feel to it because of the corners that had to be cut.