I have two macros to trigger Expose and Application Expose.
Middle mouse click will trigger Expose.
Ctrl + Middle mouse click will trigger Application Expose.
In the Expose macro, if I choose "ignoring modifiers", I will get a conflict palette with Application Expose macro when I press a Ctrl + Middle mouse click.
Middle mouse click itself will correctly trigger Expose and no conflict palette.
I have to modify the Expose macro and choose "with these modifiers" and not click on any modifiers, as such:
With this choice, there is no conflict palette when I perform a Ctrl + Middle mouse click.
"Ignoring modifiers" literally means just that. The middle-click is the trigger, regardless of what modifiers may or may not be down. This lets you have one macro, triggered by the middle-click, that can then do different things depending on what modifiers were down when you clicked -- any modifiers are included in the %TriggerValue% token.
And, as you've found, if you want it to only trigger when no modifiers are down you have to say "pay attention to the modifiers and make sure they are not down".