geometry - Getting rid of exceptional fibers by passing to finite covers?

If the Seifert fiber space is compact, then this is true, as long as the base orbifold is "good", which means that it has a finite-sheeted manifold cover, which is a compact surface. This induces a cover of the Seifert fiber space which is a circle bundle over the surface. If the base orbifold is bad, then no such covering will exist. This can happen for a Seifert fibering of $S^3$ over a football orbifold with distinct orders of torsion points, or over a teardrop orbifold.
If the Seifert fiber space is non-compact, then there may be infinitely many exceptional fibers, and the base orbifold might have torsion of arbitrarily large order, so there is no hope of finding a finite-index cover which is a circle bundle.

See the draft of Thurston's book for more information on orbifolds and Seifert fibered spaces. Exercise 5.7.10 is on the Seifert fibering of $S^3$ over bad orbifolds.