for example i started a game with 600% difficulty level and these are the errors that popped up within a month of play.
Note that (I'm pretty sure that) the difficulty setting only changes the size of alien populations/economies - it does NOT change the amount of minerals in the alien home world. If you change NPR populations significantly, (my feel would be greater than 2x, i.e. 200%), then there's a good chance that you're going to break the game. In other words, if you keep banging your head against the wall and it hurts, then stop banging your head against the wall.
If you want a more difficult game, then try a conventional start. I would actually try it with 0 NPR (so that the initial NPR doesn't burn up all the precursors). When you encounter an alien NPR that occurs through system generation, they'll be a LOT more technically advanced than you are.
You can also run the NPR empires yourself. I realize that this takes away a lot of the "fog of war" stuff, but you're a lot smarter than the computer will ever be, and so you can give your empire a much tougher time (assuming you can role play well enough to get into the heads of the aliens and your race and compartmentalize information the other shouldn't know).
John
PS - Is there a particular reason you chose to post this in Bugs as opposed to The Academy (since it's phrased as a question rather than as a bug report)? If you wanted to make a bug report, then you should make sure to save your DB regularly so that you can send Steve a DB and then make the report in the official thread. I suspect you're right that things are broken when NPRs run out of minerals - this was a much worse problem when AI NPRs were first introduced - but the only way it's going to get fixed is to send Steve a DB where the error is happening and let him see the code fail.