I'm fully aware that editing is quite different from creating a new route, but unfortunately in this case it has an enforcement purpose.
No alliance is directly allowed to exceed the quota, to my knowledge this is not happening through any bugs that I'm aware of, (if it is due to a bug, please any information can be helpful). However, there is an oddity associated with alliances which allows this to happen.
When a player in an alliance:
A. shuts down an alliance base
B. Leaves an alliance
the alliance routes which would now be 'impossible' are allowed to live.
Why?
When a player shuts down an alliance focus city, all fellow alliance members' routes "shouldn't" exist anymore. It's impossible to force a player to leave a focus city open because of an alliance member's routes. At the same time, it's unreasonable to allow a player to unexpectedly exert control over another players routes, so we cannot automatically close down these routes. Both of these options boiled down to the belief that we cannot make a system which forces sudden, direct and unexpected alterations to a player's airline (Either closing a route or forcing an unwanted base to stay open) by the actions of another airline. Leases, as an antonym, are relatively predictable, are fully the result of two player's conscious & active decisions (to lease out or in), have several warnings for automatic recall processes, and can cause relatively little harm when returned unexpectedly early. As an alternative we allow the routes to stay open, but unless there is a viable method for that route to exist (i.e. another alliance member has the same base, or it serves one of the route operator's own bases) the editing is locked until the route is closed.
When a player leaves an alliance, it is difficult to close routes that are operated from alliance bases to prevent fracturing route structures. There may be logic issues causing errant or illogical behavior to occur. Say a player operates only three routes on an aircraft... A to B, B to C, C to D. Airports A and D are the player's focus cities, B is an alliance member's (assume C is nothing). If they quit the alliance the route B to C becomes impossible because the player has no base at either B or C. Closing only B to C means the plane's remaining routes are disconnected, the script cannot rationally decide whether it is preferable to close A to B or C to D, but B to C is still an impossible route. Admittedly there are a certain, select few scenarios which may cause disconnected routes, but they're far more difficult to achieve. When this player joins a different alliance, it brings along these residual alliance routes which may push the alliance past its limit. Perhaps we need to review this scenario to prevent a player leaving an alliance until this is reconciled in advance... I'll see what I can do, but unfortunately I'm booked for the night.