Example:

fn a() {}
fn b(_: Query<&mut Foo>) {}
fn c(_: Commands) {}
fn d(_: Query<&mut Foo>) {}

app.add_systems(Update, (a, b).chain());
app.add_systems(Update, (c, d).chain());

In this example, systems b and d are ambiguous. However, since c has commands, an apply_deferred stage will be inserted between c and d. This accidentally resolves the ambiguity between b and d since b and d are now separated by an apply_deferred.

If however we add mut commands: Commands to a, b and d will now be reported as ambiguous! This is confusing since we never touched b or d! In fact, user code (not just internal Bevy code) can induce ambiguity to appear just by add before/after constraints on Bevy internal systems.

We should at least get Bevy internals to be resilient to this!

Discord discussion: https://discord.com/channels/691052431525675048/749335865876021248/1491243586082181312