Here's a few things that may cause that...
Corroded/dirty battery terminals
Loose battery terminals
Loose ground - either at battery or at alternator - engine ground strap loose, missing, dirty, or frayed.
bad connections at the alternator
Possibly voltage regulator problems?
Bad relay somewhere
Bad battery (broken internal connections - may be intermittenet, bad cell in battery - won't charge over 11V, etc).
Thermal breakdown of a wire or connection somewhere in the engine bay due to one of the above conditions.