I wouldn't say that chances for Dinamo to qualify for CL were small even after the first game, its just that putting money on them (or in this case chosing them) was not the optimal choice.
With a little bit more composure and luck Dinamo could have finished the job in the first game (game would imo end much different if Zajc didn't hit the bar at 2:0) and even in 2nd game they weren't without their chances and it could very well end up different. Biggest downside of not qualifying for CL is that Dinamo will most likely have to sell someone by the end of transfer window.
When I said that there is a small chance for them to qualify, I meant after the first game. Of course that everything would have looked different if they had kept the 2-0 lead in the first game. But when Viking managed to equalize in the first game, I had a feeling that Viking have much higher chance to qualify than Dinamo. It's mainly because of the artificial grass (like cryptofrka said). In some games in earlier seasons all Croatian clubs had problems playing on it. I don't know why.
Dinamo doesn't have financial problems, but like almost all other clubs of its rank, it has to sell players in order to cover the budget, and also we don't have any big stars in the team at the moment who have, let's say "ooutgrown" the club and want to leave.
That's just reality when you are not owned by a billionaire and instead you are mid range club from a small country, controlled by its fans (somewhat similar to Spanish socios model). Previous management wasn't as responsible and they took many risks, but new one wants to play it safe in order not to endanger the club in the long run.
/snip
Dinamo depends on their scouts noticing new talents before they were noticed by someone else. Just look at Olmo. He came to Dinamo from Barcelona because he couldn't find his place in the first team. Then he played great in Dinamo and Salzburg and look at him now. Unfortunately there is no way for Dinamo to keep players like Olmo after they "outgrow" the club and then the process starts all over again (find a young player, train him to become a star and sell him).