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Either there were no problems and therefore nothing to fix.
Or there were some problems are therefore something to fix.
But how can apparent problems be fixed?
Unless "apparent" in this context means "obvious"? I'm confused!

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from http://www.m-w.com/dictionary/apparent :

1: open to view : visible

2: clear or manifest to the understanding

So, yes, they've fixed all the problems that were immediately obvious. There may be other problems that the first set of problems were hiding or that aren't really discoverable from a quick glance, so you shouldn't necessarily expect a perfect experience.

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Apparent is one of those words that meaning has morphed because of the situations they are used in.

Apparent means visible, but how it's used doesn't necessarily mean that. In modern terminology, an "apparent problem" is "a known problem" or "a problem that is thought to exist." You could say obvious, but I think "known" is more accurate. It doesn't have to be obvious to be known, and therefore apparent.

The person is being careful not to claim that all problems were fixed -- only those he was aware of. To his knowledge, the thing (program?) is completely fixed.

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The expression, as used, asserts that a problem was fixed while expressing a degree of uncertantity as to whether the fixed problem was the underlying problem.

You asked "How can apparent problems be fixed?" I'll give you a real-world example.

You pass out at work. Testing in the hospital reveals you're dehydrated, which is corrected by an IV.

While the doctor doesn't know your dehydration was just from to excessive sweating while working in the heat, lacking other symptoms, the low probability of an underlying illness would not justify the cost of further testing. The doctor would state that the "apparent problem was fixed."

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I've probably used this expression myself several times over the years. I know exactly what I mean by it. I can't say for sure everyone else would mean the same thing, but I think I've normally been at pains to explain myself to whoever I was talking to when I said it.

Say a user reports a problem with some software I'm responsible for maintaining. His definition of "the problem" might just be "the software crashed". I might have a very limited budget for solving it. I might quickly discover that the proximate cause of the crash was, say, an attempt to divide by zero in a context where according to the system specification, the relevant program variable should never in fact be zero.

I might just add a quick and dirty line of code to test for and avoid dividing by zero. Perhaps I'd assume a meaningless result of zero instead. Hopefully I'd add a comment explaining why I added that test, and if possible keep a copy of the data that caused the error (just in case there's a budget to investigate more thoroughly somewhen in the future).

In this situation, I might say I've "fixed the apparent problem" (the crash), knowing and intending to convey that there must be an underlying problem that hasn't been fixed.

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In this particular case I think "Apparent" is equivalent to "illusory".

That is they saw what they thought was the problem and took action to fix it. However it turns out that this was not the real problem and there actions did not fix the underlying problem or may have made thing worse.

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