The AI may have Red bases with upgrades through modules, among other possibilities.
One way to check is to click for details on the AI ships, count the weapons, add the attack factors, and compare the result with the "nameplate" value those weapons would sum to. If the reported value is higher than the "nameplate" value, then the AI has augmented the attack factors.
Red bases are one way. Another source of upgrades comes from surveyed anomalies. Another way is in the race setup screen, where one can allocate race points to a higher attack factor that modifies all ships, I believe.
OTOH, if the reported value is the same or only slightly greater than the "nameplate" value, then the AI is simply ahead of you in weapons research. Is the AI putting any defense on the ships?
Note also, that a planetary defender really does not need engines, which would free up space for weapons, etc. I find that a help early, when the AI is trying to attack my planets.
