Yes, online/automated converters often put some ugly coding when converting… especially if you are using a pdf as your source doc.
You can easily replace those spans in Sigil using the tag-mechanic plug-in. Also, if your paragraphs all have a basic <p> tag then all you need to do for your spacing is add the
p {text-indent: 1.2em}
to your attached style sheet.
If it is not a basic paragraph tag and has something like
<p class="calibre2">
Then you can do a simple find/replace to fix it:
Find: <p class="calibre2">
Replace: <p>
Should take about 30 seconds to do all that in Sigil.