After finding a problem with something, what is the most appropriate way to alert a moderator if you do not have any reputation? Would it be a good idea to post the problem at all even if it is not in the meta section?
You don't always need to ask a moderator. I tend to often just pop on the appropriate channel on chat, and ask very politely about it. This might include things a low rep user (well I am on other sites) can't fix such as REALLY minor annoying spelling mistakes and so on. In short, if you're familiar with the site, there's always ways around low reputation (for good, not evil). If its important, there's always ways to do this. Neither this, nor the other question that's referenced in the comments quite counts as 'urgent'
On the other hand, you need 5 reputation to post on meta. One upvote of any sort should do the trick. Post a quality answer and you can easily get a lot more than that. Ask an awesome well documented question (or one that people find interesting). Using the site will give you the rep to do what you need.
In a sense reputation isn't just how much people on the site values you. Its also a reflection of the involvement you have in and with the site in many cases. Meta access has a trivially low barrier of entry that anyone who even tries will reach - and well, you've reached it yourself now.
While there's a certain amount of leeway granted to low rep users, and other users try to help things get shifted to the right place through flagging and other methods, this of course does not mean its fine to ask SU questions on meta, or vice versa. Its not a good idea to use the main site to post meta questions on the assumption it would be moved - if it isn't an issue of utmost urgency, it can wait till you get that 5 reputation.