I think that this must be some freakish ocuurence. The way you describe it, there isn't anything you did wrong, unless maybe if you have been throwing in spices by the handful.
Tomatoes (incl. skins) don't contain anything thickening. In fact, when you want to thicken a tomato puree, you are in for hours of constant stirring over gentle heat until most of the water has evaporated. It's still not jellylike after that.
They shouldn't turn brown either. Carotenes are not terribly heat sensitive. Some of them will degrade, dulling the color somewhat (you can't keep the color of raw tomatoes), but the change won't be too big, it should be still more red than brown. That change won't be affected by oxygenation anyway, so lemon juice won't help. In my experience, enzymatic browning (which is affected by oxygen presence) just doesn't happen in tomatoes, you can leave a cut tomato exposed to air for days, and it won't brown the way apples or avocadoes do.
You could be experiencing some browning due to a Maillard reaction, but tomatoes are low in carbohydrates, so for this to produce any significant browning, you must be terribly overheating it. And by "terribly overheating", I mean it's one step removed from charring.
The practice supports this, here is the color you can expect from tomato puree which has been cooked for a while:
Garlic tends to turn blue-green when cooked in the presence of acid, and the combination of red and green should look brown, but if it affects color significantly, you are using way too much garlic. If you insist on using lots of garlic, you can try adding canned garlic after the tomatoes have been cooked, before the pureeing, or adding garlic powder to the prepared soup.
The only thing on your list which could have thickened is the pepper. Again, you must use powdered dry pepper it in amounts comparable to the chille powder in chilli dishes in order to experience a significant thickening. If you do this, and insist on this amount for taste reasons, but want a thinner soup, you just need to make it more dilute. First, don't remove the seeds of the tomatoes. Second, consider using fresh peppers instead of powder (either pre-roast to charring and remove the skin, or sautee to soften together with the tomatoes without removing the skin). Third, if all else fails, dilute with vegetable stock or some other liquid (commercial vegetable juice, whey, or herbal tea).
If you didn't overuse garlic and/or pepper powder, but the problem persists, there is something wrong with some of the ingredients. Try tomatoes from another source or something. But chances are that it was a one-time problem.