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Most software systems developed nowadays are highly complex and subject to strict time constraints, and are often deployed with critical software faults. In many cases, software faults are responsible for security vulnerabilities which are exploited by hackers. Automatic web vulnerability scanners can help to locate these vulnerabilities. Trustworthiness of the results that these tools provide is important; hence, relevance of the results must be assessed. We analyze the effect on security vulnerabilities of Java software faults injected on source code of Web applications. We assess how these faults affect the behavior of the scanner vulnerability tool, to validate the results of its application. Software fault injection techniques and attack trees models were used to support the experiments. The injected software faults influenced the application behavior and, consequently, the behavior of the scanner tool. High percentage of uncovered vulnerabilities as well as false positives points out the limitations of the tool.