At L. Spice's suggestion, I hereby reify (!) my comment "Fourier inversion on the real line? Too mundane?" :)
But while we're here, I'd want to remark that to my mind much modern analysis (e.g., post-Schwartz, post-Grothendieck, et al) amounts to reconsideration of seemingly illegitimate symbol manipulation that mysteriously gives reliable answers (e.g., in Heaviside's work in the 1890's and thereafter, in Dirac's physics beginning c. 1928, H. Bethe's and others' work in the early 1930s).
In that context, one might argue that the ground-breaking work of the Italian, German, and French analysts in the late 19th and early 20th century was wonderful, but did not go far enough. In particular, although (as I've ranted elsewhere or other occasions) the precisification of the notion of "function" in set-theoretic terms was an excellent thing, it was/is arguably too restrictive (witnessed already by the "almost everywhere" kludge/revelation in Lebesgue-et-al theory).
In particular, although Fubini-Tonelli's theorem can fail due to "pointwise" problems, if sufficiently recast about not-literal integrals but continuous functionals, it can be designed-to-succeed in many situations where pointwise failure is irrelevant. Thus, in many practical situations, a "literal failure"'s incorrect conclusions can sometimes be salvaged by not being sucked down into the miasma of (irrelevant) pointwise issues.
To my mind, an archetype for this is Clairault's theorem on the interchangeability of partial derivatives ... under some conditions. Naturally, at the time, and still nowadays for many, this is a pointwise issue. However, taking Fourier transforms, we find that distributionally the derivatives are always interchangeable.
Back to the immediate question: another number-theoretic example (which I included as a prank-question in my old book on Hilbert modular forms) is about the "inner product" (which it cannot literally be...) of a holomorphic Poincare series and a holomorphic Eisenstein series. The seeming paradox is that if we unwind the Eisenstein series, we (correctly) compute the zeroth Fourier coef of the Poincare series, which is (in the holomorphic case only!) $0$. But, if we unwind the Poincare series (which is not ok... ) we seem to compute a higher Fourier coefficient of the Eisenstein series, thus, seeming to show that Eisenstein series are constants. The fallacy is that the Poincare series cannot be unwound here because there was cancellation in the summing of it: when unwound, Fubini-Tonelli does not apply, and, indeed, the seeming conclusion is incorrect.
The non-frivolousness of that example resides in a standard procedure in analytic number theory (and in automorphic extensions of the classical versions thereof) where both Eisenstein series and Poincare series are extended by a sort of Hecke-summation device to depend on a complex parameter $s$, and wherein a fairly arbitrary thing is "wound up" to make an automorphic form, and then spectrally decomposed, etc. It is common practice to simply ignore convergence issues in such spectral expansions, with a few exceptions. And, indeed, even in the tiniest cases, $L^2$ convergence is some distance from pointwise, but the discussion is all too often pointwise.
Another archetype is the spectral decomposition of pseudo-Eisenstein series (in various contexts) in terms of genuine Eisenstein series. This decomposition in the simplest cases is derived from ordinary Fourier inversion applied to test-function data for a pseudo-Eisenstein series, with the idea to wind up this expression to an integral of Eisenstein series. The obstacle is convergence. Thus, the Fourier-Mellin inversion path is moved sufficiently far to the right to legitimize the winding up (by Fubini-Tonelli, for example), and then the path is moved back to the critical line. The small surprise, which may seem innocuous in the simplest cases, is that residues of the Eis appear. For $SL(2,\mathbb Z)$, the residues are essentially constants, which may be misleading. Namely, for higher-rank groups (e.g., $SL(4)$ or $Sp(4)$, the residues are highly-nontrivial automorphic forms (Speh forms).
(The previous are arguably even-simpler issues than difficulties in evaluating traces in the obvious fashion.)