Can you provide details on which primer set you used to generate your sequence data? Many primer sets will amplify off-target sequences. That is just the nature of the process. How much of your sequence data is being returned as Bacterial? Few? Many?
I would advise against removing removing groups of taxa just because your are unable to identify what you want. In fact, it is best to leave these "outgroup" taxa within your database. This way you can more confidently remove off-target sequence data. Otherwise, you may falsely classify many sequences as simply Eukaryotes, when in fact they are not.
What sequencing protocol was used? That is, is your sequence data in mixed orientation? This can fool you into thinking your data are composed of bacterial sequences. See the following forum threads:
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