Possibly. But it's easier to explain what should be happening here:
- JIRA Core is a full service which acts as a server application providing the Core functions of JIRA, AND a framework for other JIRA Applications to run on. You install it on it's own on a physical or virtual server.
- JIRA Software is a JIRA Application that runs on top of Core. You install it in a Core installation.
- There is a download for JIRA Software which is a simple bundle of both - think of it as Core with Software already installed and configured.
- You can buy licences for Core and Software separately, but Software licences include Core access. You do not need any Core licences to make Software work (Example: you could have 25 Core users and 50 Software users - this would be 50 people with access to Software functions, and 75 with access to all the Core stuff).
To upgrade Software, you can install a new version of the application from within JIRA, using "manage applications". Or you can get a new download and tell it to upgrade the existing installation (in which case it may also upgrade Core if the version is newer)
Core can only be upgraded by running the installers in upgrade mode.
I would not expect a message that Core is incompatible whatever you've done, more that Software is not compatible with Core. Unless you've done a manual install, or your licences are a mix of valid and expired, which could get weird.
Could you show us the text of the error message? And tell us what your versions are?
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