Its a fairly simple issue. "you are dominating me" = you are winning a war. This discusses actual results; aka what your nations do to each others.
"might score" and "your army is very weak" are two scores based on hypothetical calculation of your empire's and army's strength in the aggregate. With the former (apparently) including cities and tech and probably armies (unlikely but possible income and cash). And the latter only armies. This is a hypothetical value not a results based value; aka what your nations think of each other, tactically. Think of this as their advisors saying "their armies are weak"
In theory, even if th numbers are PERFECTLY ACCURATE you could still have the situation described by the OP by employing superior tactics or just getting lucky (ex: your inferior army flanks them while they are caught up fighting an elemental lord or another player or just not engaging you since they are to the north and you swept in from the south)
In practice they will always be this way in a game between a human and AI. The problem is the empire strength score is irrelevent in the age of supersov/superstack dominance and so are armies. Your army is very weak because your army is only your sov and maybe some heroes, while every Ai faction has dozens of cannon fodder (spearmen) artificially inflating the score without having any releveance to combat at all.
It would be interesting if instead of saying "your army is weak" it said "our advisors estimate our army is stronger" and instead of "you dominate me" it would say "you won recent battles". That ensures both numbers can co-exist without contradiction.
