Let $E,F$ be two smooth vector bundles of the same rank over a smooth compact manifold $M$.
Does there exists a weak isomorphism $\Phi \in W^{1,2}(M,E^* \otimes F)$ between $E$ and $F$?
i.e I am asking if there exists a bundle morphism $\Phi:E \to F$ which lies in a suitable Sobolev space, and is an isomorphism (of the fibers) almost everywhere.
For a concrete example, we can start with $E=T\mathbb{S}^2, F=\mathbb{S}^2 \times \mathbb{R}^2$. Is there a measurable global frame on $T\mathbb{S}^2$?
Of course, in the smooth category what I am asking is nonsense- the point is that I am interested to know, if, when weakening the regularity requirements every two bundles of the same rank are indistinguishable.
You can get something even better. Ignoring sets of measure zero, all vector bundles are smoothly isomorphic.
Let's consider first your specific example of $TS^2$. Think of $S^2$ as the unit sphere in $\mathbb{R}^3$ and let $X_1(p)$ be the orthogonal projection of the vector $e_1 = (1,0,0)$ onto the tangent plane of $S^2$ at $p$. This is a global vector field on $S^2$ which vanishes at two points $(\pm 1, 0, 0)$. Take $X_2(p)$ to be the orthogonal projection of the vector $e_2 = (0,1,0)$ onto the tangent plane at $p$. This is again a global vector field on $S^2$ which vanishes at two points $(0, \pm 1, 0)$. The locus of points at which $X_1,X_2$ are linearly dependent is precisely the equator $\{ (x,y,0) \, | \, x^2 + y^2 = 1 \}$ so the map $S^2 \times \mathbb{R}^2 \rightarrow TS^2$ given by $(p,(a,b)) \mapsto aX_1(p) + bX_2(p)$ is a smooth bundle map which is an isomorphism of the fibers away from the equator.
This situation is actually quite general and generic. Given a rank $k$ bundle $E$ over $M$, one can define the submanifolds $\Sigma_r \subseteq \operatorname{Hom}(\mathbb{R}^k, E)$ which consists of bundle morphisms of rank $r$. Those are smooth submanifolds of codimension $(k - r)^2$. It turns out that a generic section $s$ of $\operatorname{Hom}(\mathbb{R}^k,E)$ intersects the submanifolds $\Sigma_r$ transversally so the degeneracy locus
$$ \mathcal{D}_r(s) := \{ p \in M \, | \operatorname{rank} s(p) = r \} $$
is a smooth manifold of codimension $(k - r)^2$. In particular, the singular locus $$ \Sigma(s) := \{ p \in M \, | \, \operatorname{rank} s(p) < k \}$$ is contained in the union of submanifolds of positive codimension and so has measure zero. Such a generic section will give you a smooth bundle map which is an isomorphism away from a set of measure zero between $E$ and the trivial vector bundle.
To see that $\Sigma_r$ is a manifold, let's argue first why the space $\Delta_r$ of matrices of rank $r$ is a smooth submanifold of $M_k(\mathbb{R}) \cong \mathbb{R}^{k^2}$ of codimension $(k - r)^2$. Set
$$ U = \{ X \in M_k(\mathbb{R}) \, | \, \text{the top } r \times r \text{ minor of } X \text{ is non-zero} \}. $$
Then $U$ is an open subset of $M_k(\mathbb{R})$. Let's describe both a chart for $U \cap \Delta_r$ and a locally defining function. Take a matrix $X \in U \cap \Delta_r$ and write it as a block matrix
$$ X = \begin{pmatrix} A & B \\C & D \end{pmatrix} $$
with $A \in M_r(\mathbb{R}), \det(A) \neq 0$.
Performing "block Gauss elimination" to eliminate $B$, we get
$$ \begin{pmatrix} A & B \\ C & D \end{pmatrix} \begin{pmatrix} I & -A^{-1}B \\ 0 & I \end{pmatrix} = \begin{pmatrix} A & 0 \\ C & D - CA^{-1}B \end{pmatrix} $$
but since the rank of the right hand side is $r$, we must have $D = CA^{-1}B$. This gives a local chart $\operatorname{GL}_r(\mathbb{R}) \times M_{r \times (k - r)}(\mathbb{R}) \times M_{(k - r) \times r}(\mathbb{R}) \rightarrow U \cap \Delta_r$ of the form
$$ (A,B,C) \mapsto \begin{pmatrix} A & B \\ C & CA^{-1}B \end{pmatrix} $$
and a locally defining function $f \colon U \rightarrow M_{k-r}(\mathbb{R})$
$$ f \begin{pmatrix} A & B \\ C & D \end{pmatrix} = D - CA^{-1}B $$
so that $f^{-1}(0_{(k - r) \times (k - r)}) = U \cap \Delta_r$. This shows that $U \cap \Delta_r$ is a submanifold of codimension $(k - r)^2$. Since a rank $r$ matrix must have some non-zero $r \times r$ minor, the argument above can be applied after permuting the coordinates around any rank $k$ matrix showing that $\Delta_r$ is a submanifold.
Finally, the argument above works as well for families and allows you to show that $\Sigma_r$ is a submanifold of codimension $(k - r)^2$.