What specific type of packaging are you using - is this aseptic bag in box/drum?
Is it shipped ambient?
What is the road infrastructure like in the receiving country?
I do know of examples where bags have been fine for domestic / local international distribution, but extended transport, particularly if the roads are very rough at the receiving end, can subject the packaging to more stress than has previously been the case. This can sometimes cause very small pinhole breaches / cracks to form in the bag structure over time, which then allows contaminants in.
The way to address this is to minimise any room for movement of the inner packaging - e.g. use of (appropriate!) padding in the tops of drums to fill the gap under the lid if there is one, or very carefully sized boxes.
Changing the grade of bag film may also help, and indeed some manufacturers offer different laminate structures that range from cheap/thin that may be fine locally, through to more costly but far more robust variants that can be very useful if the product is potentially going to be subject to more physical stress in distribution.
With concentrates moved at ambient temperatures, if there is any headspace in the bag you can also potentially get condensation forming, and this can then drip back onto the surface of the concentrate. This creates regions that are slightly more dilute than the bulk of the concentrate, where it is then potentially easier for micro growth to get started as the aw is higher. This can also make representative sampling more of a challenge, as a sample taken from the "bulk" part may still show a fairly low count even thought there are parts of what would nominally seem to be a homogeneous liquid where the count is getting to a level where there is noticeable gas production.
It's therefore probably worth checking how the samples were drawn, and also worth clarifying with the lab exactly what methods they've used for the analysis - I've seen two different TVC approaches give counts that differed by 104!
It might also be useful to know what the rest of the assessment of the problem stock found - e.g.
Any sign of reduced Brix level compared to when it was packed?
Increase in lactic acid, acetic acid, and/or ethanol content?
Presence of any off-notes or unusual flavours?