@jheindel has given an insightful answer. I want to supplement it with some mathematical analysis. Szabo and Ostlund note that the kinetic energy integral over two primitive $s$-Gaussians $A,B$ is equal to$^{[1]}$
$$
\left(A \left| - \frac{1}{2} \nabla^2 \right|B\right) = \frac{\alpha\beta}{\alpha+\beta} \left[ 3 - \frac{2\alpha\beta}{\alpha+\beta} \left| \mathbf{R}_A - \mathbf{R}_B \right|^2 \right] \cdot S_{AB}
$$
where $\alpha, \beta$ are the Gaussian exponents, $\mathbf{R}_A, \mathbf{R}_B$ are the centers of the Gaussians, and $S_{AB}$ is the relevant overlap integral, which we know is greater or equal to zero. The term inside the brackets can become negative, rendering the entire integral negative.
For more insight, one may do the following:
- Graph a one-dimensional Gaussian. Observe that it is positive everywhere. (The results translate to three dimensions.)
- Apply the kinetic energy operator to the Gaussian from step 1 and graph it. Observe that there are negative regions.
- Multiply the result from step 2 with a second Gaussian. Observe that depending on the center of the second Gaussian, one can amplify the negative sections and suppress the positive sections of the result of step 2. By taking the integral over all space, one can obtain a negative total value.
[1] A. Szabo, N. Ostlund: Modern Quantum Chemistry, Dover Publications, 1st. edition, revised, 1996, page 412.