my short answer is that your team simply isn't as good as you think, you have lots of flaws and weak links.
longer answer--
pitching: as a team,
That's not going to get it done. Of your 7 pitchers with 100+ IP, 6 have ERAs 4.50 or higher, three have ERAs 6.50 or higher. Elevate the pull rating for all your SPs to 4 (Charlton and Alexander can be 3) and elevate all your RP pull ratings to 5. Roster 14 pitchers instead of 12. This gives simmy the opportunity to play LvL and RvR more frequently in key spots and saves runs over the long haul. Don't use a ClA, set your best 2-3 relievers to SuA
defense: 67-28 ratio, .983%
Your only 3 players consistently generating + plays are your 1B LF and CF. CF defense is super important but you're going to want to see if you can find guys who will consistently save runs at all 7 positions (P and C don't really generate + plays). Your SS 3B RF and 2B are all generating - plays, I think you're actually getting a few of the +/- where they make errors on the same play as a + ...
Wallace is useless, bench him. Spehr should probably be on the bench too esp vRHP. Good shortstops (85-85-90-90 with a .700+ OPS) can be quite hard to acquire.
Playing the incorrect defensive alignment is losing you games. Alonso would be best at 2B, Costilla would be best in LF, Bernadina would be best at 1B, Fister would be best at RF, you don't really have a true 3B on your roster at all. By trading away a few of Alonso's plus plays in LF, you're erasing the negative plays at three other positions. And Costilla will still get his share of + plays in LF himself so it's not a huge loss. Those runs seriously add up,
offense:
Is actually quite good, I can't say too many bad things about that. 80 caught stealings is probably way too many, maybe consider stealing less aggressively. At coors you can afford to play more station-to-station because your hitters are so productive on their own, you don't really have to manufacture like you would in a cave like Seattle