First of all, ensure you don't have any planets that you forgot to get population upgrades for. The underdevelopment tax, even if it's just on a handful of planets, will totally kill you.
Second of all, it seems from your description your economy probably isn't well-planned. Each income building (trade port, refinery, and to a lesser extent culture) works differently, and you want to build them in different places.
Culture spreads out from the planet it's built and can affect a large number of nearby planets. Multiple culture buildings don't stack for effect, they only make culture spread faster, and can overpower enemy culture to push it back. If we're talking about the "core" of your empire where these are non-issues, you can build one culture generator for every 6 or 7 planets. One per planet is total overkill. On the front lines you'll definitely want more, but in the back you don't need it.
Refineries will dispatch service ships to every friendly extractor in a 1-jump radius, improving resource income. The problem is, each extractor can only be serviced by up to 3 refineries. Any more will have no effect. This means that you need to space out your refineries such that they don't interfere with each other. Generally you pick one good location and build three refineries there, then don't build any other refineries on nearby planets in order to avoid conflict.
Now, trade ports are the only way to build truly massive incomes. If you've noticed, I've told you to build refineries and culture sparingly, so this should make up the vast majority of your late game income. You can build as many trade ports on the same planet as you like, the important thing is picking planets where you don't build trade ports. The idea is to create artificially long trade routes, which boosts the income of all your trade ports.
Traders take the shortest route available to them, while passing only through planets with trade ports. This means that if you build a trade port that creates a shortcut through the middle of your empire, you could accidentally reduce your trade route length. You can make more money by artificially inflating your trade route length and leaving some planets empty of trade ports.
Beyond that, it's difficult to say what your problem is. If you're at maximum upkeep (75%) that's going to be a huge drain on your economy, and if the AI is well developed they could outperform you, though a smaller fleet will get trounced by your larger one. I don't know how big the AI's empire is or how well-developed it is, and often times these ratings can be deceptive. I've played entire games as "last-place" economy only to find out in the end-game statistics that I was only behind by like 1 credit per second the whole time. The problem is you just don't know whether you're very close to your rivals or way behind them. Especially with empires this large, you just can't count up their assets and figure it out in real time to make the comparison.
