Ah, ok, for an ambient-stable product you need to be a bit more thorough in the approach, as any presence of viable yeasts, moulds, and certain types of bacteria will very happily grow in a warm environment with plenty of nutrients available. My experience has been that pineapple is exceptionally good at fermenting and at growing mould, so it does need to be approached with caution.
As a first stage I think it's critical to get some microbiological data to understand what the current situation actually is. Appreciate that this will take a little while to organise and test, so please feel free to post back here in a week or two once results are available :)
As this isn't a pure juice product, if you're permitted to use any preservatives in this type of drink then I'd look into this too. I wouldn't assume these will stop everything, as they definitely won't, but they can help provide an extra defence against things that might otherwise cause a problem.
To get to ambient stability with a cold-filled product, you need to ensure that your product is clean, your bottles are clean, and the environment in the process area is clean - if there is any microbiological contamination of the bottle, or the environment is such that there are lots of yeasts and moulds floating around in the air, then these will multiply rapidly if they get into your juice.
I'd suggest working through your process one stage at a time, looking at what you can do to optimise each stage. As I'd noted above, I'd have a look at fruit washing, at your pasteurisation process, and at bottle washing. Also go back one step before fruit washing and make sure that your sorting process is working reasonably well, as having lots of e.g. mouldy fruit around is going to intro another source of potential issues into your process and factory.
Given that you're aiming for ambient stable end product, the filling process is also worth scrutinising, as at this point there are no further processes that will address contamination. Preservatives can help, but I wouldn't rely on them too much. When you say the filling is done manually, how is this physically done?
There are some plastic bottles available that can be used for hot filling, so this could also be worth investigating.