The fact that they have thousands of ships but only have 1 or 2 ships guarding there most vital planets! Fix your defences!
Thousands of starships are a fact? How? What we get from the episodes and movies (including the apparent lack of starships near earth) suggests the opposite, a rather small starfleet. And in the 23rd century even more so than in the 24th.
You jokeing right?
The federation spans I believe afew hundred odd light years do you even understand how vast 1 light year is?
As I said in another post think of all the dutys:
VIP transport and escort
Exploration
Border patrol (must take hundreds or possibly thousands of ships seeing as it borders are huge)
Humanitarian aid and disaster relief.
Diplomatic missions
Anti Piracy and other policing duties
Monitoring and surveying natural phenomenon
Monitoring and spying on local and external threats
Guarding the frontier
Anti Terrorism
Dangerous cargo transport
Starfleet would need at least 1000 ships operational at any given time dureing a complete peroid of peace!
Saying starfleet would have a few dozen ships would be like saying the US navy could do its job with 6 Frigates and a couple of supply tenders
Also look at the registration numbers by DS9 they are up in the 20000's and its established they reuse some registration numbers. So your looking at most likely 1000 Miniumun right up to 25000 maximum.
To me its senisble to assume its around 5000-10000 including support ships.