Liquibase update from java code gives ChangeLogParseException

2. Caused by: liquibase.exception.ChangeLogParseException: Error Reading Migration File: Found 2 files that match liquibase/root.changelog.xml
3. at liquibase.parser.core.xml.XMLChangeLogSAXParser.parseToNode(XMLChangeLogSAXParser.java:112)
4. at liquibase.parser.core.xml.AbstractChangeLogParser.parse(AbstractChangeLogParser.java:17)
5. at liquibase.Liquibase.getDatabaseChangeLog(Liquibase.java:215)
6. at liquibase.Liquibase.update(Liquibase.java:192)
7. at liquibase.Liquibase.update(Liquibase.java:181)
8. at nl.procura.inn.web.servlets.ConfigServlet.updateDb(ConfigServlet.java:125)
9. ... 14 more
10. Caused by: java.io.IOException: Found 2 files that match liquibase/root.changelog.xml
11. at liquibase.util.StreamUtil.singleInputStream(StreamUtil.java:189)
12. at liquibase.parser.core.xml.XMLChangeLogSAXParser.parseToNode(XMLChangeLogSAXParser.java:93)
13. ... 19 more

I'm using Netbeans 8.0.2 (on Windows 7) running my web application. And that's seems to be the problem. When I deploy the war-file myself by copying this file into my Apache Tomcat server (version 7.0.57), no exception is thrown.
Also when I run the application by Netbeans but deleted my liquibase folder (with the changelog files) in the target directory (target/classes/liquibase) no exception is thrown. This target directory is of a different maven module than that of my web application.

While writing about this issue, I found out that my configuration of JRebel (version 6.0.2) caused the problem. Possibly JRebel added the target directory to my classpath somehow. By changing the configuration by just using the JRebel panel everything works fine again.

Unfortunately, it took me a lot of time to find the cause. Hopefully others with the same problem find this post.