Some programs that feed messages to SpamAssassin, such as spamc, have a maximum-size limit. Messages larger than this limit will not be processed and will be delivered without spam filtering.
For spamc, the default message size limit is 500KB. You can raise the maximum-size limit of spamc using a command-line option or a spamc configuration file (see the spamc manpage).
Other programs truncate a large message to some smaller size before sending it to SpamAssassin. If you use such a program in combination with spamc, then it should be configured to truncate at less than spamc's maximum-size limit so that spamc will process it.
The Authority Plug-In for SpamAssassin accepts very large messages but currently only processes the first 300KB. Since the average spam message is much smaller than 300KB, this limit does not significantly affect accuracy.