Debt - While a select few AI companies are successful enough to pay off their debts, most others accumulate huge debts. Many times the interest payments are higher than the AI's total income. The trouble is that the AI likes to take out huge loans even if it doesn't need it right away. In addition, new companies sometimes can't afford to buy vehicles after they've built their rails, roads, or airports. They spiral into debt and soon into bankruptcy.
Some companies avoid bankruptcy, but own nothing.
They just sit idle, borrowing as much as they can. What I mean by that is that they assess the terrain and possible actions at the instant they are about to build a section of track, rather than designing an entire route before constructing it. The route designs could have been much better if they had been planned in advance, but planning the route in advance assumes that the terrain won't change before the route is entirely constructed. It would also make it very easy for the human player to 'foil' every computer attempt at a decent route, as the human player could watch the computer-run company start to build a route, then lower or raise just one block of land in the way. The computer-run company would then have to remove all its track and start again from the planning stage.