This is typically because you have chosen an inappropriate alignment algorithm for your dataset. The standard Geneious aligner is based on dynamic programming and will be slow when presented with long sequences or large sets of sequences. In the case of large multiple alignments, you should look at MUSCLE or MAFFT rather than the standard Geneious aligner. These are much faster and still quite accurate in most cases. For aligning genomes you should use the Mauve Genome Alignment plugin, which is designed to deal with the inverted and duplicated regions that a genome alignment is likely to have.
Another operation users try to do which can be very slow is to try and align many primers against a set of sequences. The right tool is ‘Test with Saved Primers’ but this can also be really slow if they have high levels of degeneracy and lots of sequences. The section on primers will offer potential solutions.