It's not always good to increase the Civilian Infrastructure to the max right away because you will not recoup the benefits of the expensive third and fourth level improvements for a long time.  It has an opportunity cost.  Instead it would be better to increase it so that you no longer lose credits and to then increase it again once the population has started to max out.  (If you are Advent and your mothership has given you a 30% or 45% discount then it might make sense to purchase levels 3 or 4 in some circumstances.)  The money that you spend on the Civilian Infrastructure could be used to buy some more ships or something else instead, so you really want to take that into consideration.  Of course, this is all very situational; what is best will depend on your specific situation and opportunity costs.

I didn't know that about the AI.  Maybe the AI is just programmed not to suffer from underdevelopment or is programmed so that it upgrades planets as efficiently as possible.  Perhaps it's one of the AI's cheats.

It's probably a reference to both Civilian Infrastructure and also the Civilian tech tree.  Every race can do a little bit of civilian research to increase its population (above the max that Civilian Infrastructure would give you) on terran planets and some (but not all) of the other planet types.  Advent and TEC can research upgrades for Deserts and Vasari can do it for Ice and Volcanic.

The Vasari's ice and volcanic research upgrades are higher up the civilian tech tree and thus more expensive and probably not worth doing in most games.  (I only play online multiplayer against human opponents, so I rarely have more than a few ice or volcanic planets and those games don't last much longer than 1:45 anyway, so I'd proably never recoup my investment for the ice or volcanic upgrades.  But if you have several ice or volcanic planets with high allegiance and anticipate that the game will last a few more hours then it might be worthwhile.)

As a general rule, it's probably a good idea and a good long-term investment to research the two Level 1 terran upgrades for TEC and Vasari.  For Advent it's a little questionable because they have to go through one level of desert research to get to the terran upgrade.  So, it's more situational for Advent.  Maybe someone will run the numbers to tell us what the time for a return-on-investment is for that.

Hmmm... something is not right.  That doesn't happen to me.  I also checked some saved games, and I usually have a better "Credits lost to planet underdevelopment" than the AI.  Not the steep line.  Are you sure you are upgrading "Civilian Infrastructure"?  The top left box, after clicking "Develop Planet" - also the top left button.  Note you have to click twice, or upgrade at least 2 levels for all planets (besides asteroids), to get out of negative income. 

Also, are you using the current up to date patch?  The original out of the box game had some bugs, and major balance tweaks, but not that issue if I recall correctly.

Yes, there are techs in the civilian trees to improve various planet type's population by say 5% & 10% or more.  Terran population increase for TEC & Vasari are tier 1 techs.  And they are one of the best techs, in terms of pay-off time.

And a resource bonus, both crystal & metal.  Unless you want to also call that income.  But "income" makes me think dollars (credits) only.