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There are plenty of reasons why animals end up dying inside houses, and it basically comes down to one thing — all animals will go back to their nest to curl up and sleep when they feel sick or injured, and that's basically what they're doing. Rats, for example, that have ingested poison and are becoming quite unwell, will often go back to their nests to “sleep it off," except they don't. They'll die there, and rat nests are usually hidden somewhere nice and cosy in your home. So cosy that you won't be able to find it for some time.
Poison is the number one reason why animals die inside a home, so if you are using poison to solve a pest problem, you should stop. In many cases, it doesn't work very quickly or effectively, and you'll also find that it leads to a random collection of dead animals around your land. If the animals have gotten in your home, they'll be in your home. That decomposition process will start to kick in before long, and that will bring in flies, usually blow flies, as well as a smell that you won't be able to get rid of for sometime, and one that grows with intensity every day.
If poison isn't the culprit behind the dead animal in the house, it will be because the animal has managed to get itself stuck somewhere, or because you have locked them in. The latter is a common problem, usually caused by homeowners dealing up their home before making sure all animals inside have been evicted first. This can also happen when homeowners perform DIY animal removal methods that aren't suitable for the animal they are trying to target. Bats, for example, are quite fragile creatures, and incorrect handling and trapping efforts will result in sick or injured, and maybe even dead bats.
For more information, you may want to click on one of these guides that I wrote:
How much does dead animal removal cost? - get the lowdown on prices.
How to get rid of dead animals - my main dead animal removal info guide.
Example dead animal removal photographs - get do-it-yourself ideas.
Dead animal job blog - learn from great examples of dead animal jobs I've done.