1: They're fighting it from the outside, perhaps somebody/somebodies are fighting it from the inside. Used poorly this can destroy any sense of jeopardy, but then.. so can most tools.
2: Systemic failures, depend on context to find relevance. Corruption in the supply chain, soldiers & police selling off their equipment to gangs, the issues here really depend on how the Empire would deal with these sorts of issues should they occur...
If it's contemporary/scifi the government surveillance & communication channels could be routinely compromised.
3: Too little too late - The Empire can improve at those things your rebellion exploits, or at least try alternative solutions to fill the gaps in policy exposed. Your heroes are supposed to be clever, and cleverness isn't well-shown by being able to exploit the same holes in readiness over and over. Look at any extant organisation and you'll find some aspect they are trying to improve in the way they operate..and therefore you'll find a translatable trend.
If there is enough of a cultural divide/dislocation in this empire to provide grounds for an effective rebellion (as opposed to coup d'etat) it is likely that the administration of the empire is largely in the hands of those born, raised and/or indoctrinated into viewing the empire as at least 'the lesser of many evils' and that culture, as the empire, is failing & decadent. It's just not plausible for a culture to 'turn around' in a few years, so one can build intrinsic attitudes into positions of authority that allow exploitation.
Of course, it's important to keep those agents of the empire personal if they're to have any impact or value (imo) and not have them all reading off exactly the same script.
Many authors choose the approach that the evil was after all necessary, or at least an expedient way to a necessary end.
eg Brian McLellan's Powder Mage
early antagonists 'the Privileged' were asshats, but asshats trying to prevent the end of the world that noone else knew about.
Revolutions are fought by rich folks against other rich folks using poor folks, even most fictional ones are led by some long lost prince or other.
What this means is that the Empire may have it's focus on area's other than the Rebellion. The American Revolutionary War for example was preceded by many other conflicts that the British Empire was involved in, which whilst it generally came out on top, had their own costs. Rich Colonials decided they should not have to help pay for the costs of keeping themselves securely linked to european trade & produce and if anybody should tax and govern the residents of the 13 colonies, it should be them, so a Rebellion formed.
In asymmetric warfare, indeed sensibly in any kind of warfare, one naturally chooses means & objectives according to one's strengths and the opponents weaknesses. For this rebellion to succeed finally, and for your heroes to be demonstrably omgamazing, the rebellion need not succeed in every project, nor the empire fail in all of it's.
The Rebel knows they are a rebel and know what the Empire is and what it is not, they know the tools of the Empire because they are a part of it, but the Empire does not know the tools of the Rebel because it is not a part of them. The Empire will end up fighting shadows because any dissident group, any act of competence could be deliberately undermining it. It will self-harm and direct it's resources against things other than the rebellion itself.
It will seek to stave off rebel sympathies by way of reasoned argument or fear or coercion or bread & circuses not knowing that none of these matter because the author has chosen his side.
This while the rebel heroes have laser focus.