How did the Ptolemaic army disappeared ?

In the last times of the Ptolemaic Dynasty during the war between Caesar and Ptolemy XIII it seems that the ptolemaic army was comprised of ragtag bandits and roman deserters.

Were the Ptolemaic at this time unable to field a phalanx, companion cavalry, galatian kleruchs and so on ?

Now I cannot say for certain, but what I can say for certain is that in order to have an organised army you need an organised and orderly state able to carry out draft, training, equipping and so on. Mayhap that is the problem.

Well, during the Roman Expansion and afterwards, the Ptolemaioi has already reformed their armies into a 'Roman fashion'. Their armies did not exactly dissapear, they were rather eclipsed by the Romans during the end of the 1st century BC.

Maion

In any case, after the 2nd punic war the ptolemies were basically a roman protectorate which meant no need for a serious army other than for controlling riots...