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When working with lactic acid-producing bacteria, the brewer’s goal is usually to attain clean-tasting sourness, while obtaining desirable flavor contributions from these bacteria, and simultaneously minimizing off-flavors. It should be noted that off flavors span the range from undesired by most, to desirable to some. For example, isovaleric acid is a compound known for its footy aroma that would be considered an off flavor in many beers, yet it gives a highly desired flavor to certain French cheeses and is acceptable by some in small amounts in mixed fermentation beer.
With that said, contamination issues are among the biggest challenges when pre-souring wort with ''Lactobacillus''. This is because ''Lactobacillus'' does not fully ferment wort by itself (see [[100%25_Lactobacillus_Fermentation|100% ''Lactobacillus'' fermentation]]). When yeast fully ferments wort into beer, alcohol, hops, and a low pH all work together to prevent most spoilage microorganisms from contaminating the beer (although contamination can certainly happen with beer spoilage microbes such as ''Brettanomyces'', ''Pediococcus'', etc.) <ref>[http://suigenerisbrewing.blogspot.com/2014/02/fact-or-fiction-can-pathogens-survive.html "Fact or Fiction? Can Pathogens Survive in Beer?" Sui Generis Blog. 02/18/2014. Retrieved 11/10/2016.]</ref>. When fermenting with ''Lactobacillus'' by itself, either no alcohol is produced or not enough alcohol is produced to have an antimicrobial effect. Usually, hops are not used when souring wort with ''Lactobacillus'' because even small amounts of hops completely inhibit most commercial strains, but they also inhibit some spoilage microorganisms. The high available sugars, warm temperatures typically used in souring wort, and a lack of alcohol and hops , therefore , increase the chances for contamination during souring wort with ''Lactobacillus''.
Contaminates can include a variety of molds, yeasts, and bacteria. Contaminations can have a variety of potentially unfavorable flavor effects on soured wort depending on the type of microbe(s) that caused the contamination. One common off-flavor in kettle soured beers has been associated with [[Butyric_Acid|butyric acid]], which is in and smells like human vomit. Although the exact source of butyric acid in kettle soured beers has not been identified that we know of, butyric acid is produced by anaerobic contaminates and '''not''' when ''Lactobacillus'' is exposed to oxygen (see [[Lactobacillus#Effects_of_Oxygen|Effects of Oxygen on ''Lactobacillus'']] and [[Butyric_Acid|butyric acid]]). [[Isovaleric_Acid|Isovaleric acid]] is another off-flavor that can be produced by both anaerobic and aerobic contaminates.
Another common contaminate from improper wort souring is brewer's yeast (''S. cerevisiae''). Brewer's yeast is not greatly inhibited by ''Lactobacillus''. Conversely, ''Lactobacillus'' is greatly can be inhibited by the presence of active ''S. cerevisiae'' <ref name="Hubbe">[https://www.facebook.com/groups/MilkTheFunk/permalink/1407620509266159/ Effect of mixed cultures on microbiological development in Berliner Weisse (master thesis). Thomas Hübbe. 2016.]</ref>. The warmer temperatures encourage ''S. cerevisiae'' to ferment the wort quickly. This often results in a beer that isn't sour because the ''Lactobacillus'' are out-competed by the yeast. Signs that yeast has contaminated the wort include the typical signs of yeast fermentation: the presence of a krausen, a gravity shift of more than 1.005 gravity points (or 0.5-1.0° Plato), and looking at a sample of the wort under a microscope. Sources of yeast contamination can come from poor sanitation, but they can also come from the yeast manufacturer themselves. See see [[100%25_Lactobacillus_Fermentation|100% ''Lactobacillus'' fermentation]] for more information.
Another source of contamination, which is arguably desired, happens when using a "wild" source of ''Lactobacillus''. For example, when culturing ''Lactobacillus'' using non-plating techniques from grains, fruit, or from some other fermented food such as kefir, sauerkraut, etc., yeast and other microbes can carry over from the culturing process (see [[Alternative Bacteria Sources]]). The only way to guarantee that only ''Lactobacillus'' from a "wild" source such as this ferment the wort, is to isolate the microbe using plating techniques (see [[Wild Yeast Isolation]]). Otherwise, there is a chance that wild yeast will also survive the culturing process.