When integrating $y=x^2$ (ending up with $y=\frac1 3 x^3$), the values while $x<0$ become negative. Why is this?
Why does the indefinite integral of $x^2$ enter quadrant 3?
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When looking at indefinite integrals, the value at a particular point shouldn't be given too much attention. For instance, $y = \frac{x^3}{3} - 1,000,000,000$ is also an indefinite integral of your function, and it hangs out in quadrant IV for a heck of a long time for positive $x$.
Really what we care about indefinite integrals are differences of its values. So, for $f(x) = x^2$, let's assume we have some indefinite integral $F(x) = \int f(x) dx$.
Since $f(x) \ge 0$ for all $x$, then we expect (assuming $a \lt b$) that $F(b) - F(a) = \int^b_a f(x)dx \ge 0$, which is just $F(b) \ge F(a)$, i.e. $F$ is increasing. (Okay, technically "non-decreasing", but will you let me be lazy?). And yes, we can see that all possible antiderivatives are in fact increasing: $F(x) = x^3/3 +C$ is increasing no matter what value the constant $C$ has.
Implicit in your question seems to be the assumption that "when you integrate a positive function, you should get back a positive function". And that's not always true. What is always true is "when you integrate a positive function, you get back an increasing function". It's just one of the things you'll get to learn as you develop your intuition about integrating and differentiating functions.
The integral is not the area under the curve, but the signed area under the curve. Area in quadrants I and III is defined as positive, and area in quadrants II and IV is defined as negative.