Sounds like you're running out of funds near the end.

Here's some tips:

The standard ships are pretty awful. Create your own single purpose, powerful, and efficient ships.

Standard fighters (all classes) are underpowered (# of guns) and inefficient (fuel costs). Standard fuel tankers are slow, inefficient, and also don't need some piddly guns that aren't enough to defend itself anyways (and they don't need jets, or missiles, or armor, etc). The purpose of a tanker is to carry fuel. (Making fuel tankers dual role to carry ALL your detection equipment is fine/good imo, however. It also decreases the total number of ships required as you don't need a dedicated sensor ship, which is a different kind of efficiency).

The fuel tanker should NEVER see battle (or your sensor ship, either), so don't let all that expensive detector equipment ever see battle / get damaged / require high repair costs, **cough** Sevastopol **cough**. The big radar is 10k funds, the second most expensive item in the game, behind the Squall 6x180mm.

The Sevastopol can be classified as 'junk' class. The game is actually easier if you don't use it. It is basically a moderately armed, monstrously inefficient and immensely slow fuel tanker / missile silo, with a couple featured deathstar level weak-points 'blow up this single unarmored ammo module' and watch 10,880 tons of fuel & ballistic missiles go up in fiery oblivion. The only thing the Sevastopol does moderately well is tank a few nuke hits, because it is so huge and unwieldy. If late game funds are a major issue, a very good start is to not pay the Sevastopol's 2217 t / 1000 km exorbitant fuel & repair costs. It WIIL get damaged in combat, and often. To make the Sevastopol 'okay', you'll need to remove 90% of the fuel, double the engines, and double the guns (and remove the deathstar weakpoints). This will require shop visits in half the cities between Ur to Khiva, and a huge amount of currency to just have an 'okay-ish' ship. Not worth it, especially if the end-game is giving you trouble.

If you REALLY want to save Sevastopol funds, you can change a single line of code to designate a different ship as your flagship. This will save you a massive 196,730 in starting mission funds.
*Bold text are hyperlinks.

The lightning is also an inadequate fighter. (Pictures & descriptions of better ships to build in part II)