The best solution for this scenario is to edit the citation style file (CSL file). For some citation styles it is already implemented like for "Chicago Manual of Style 16th edition", where all titles are transformed to title case automatically.
If your chosen citation style does not support this, here is how to fix it demonstrated on code from the harvard1.csl file.
You need to find the macro that formats the title, usually named macro name="title". Next you need to find the lines that format the title (text variable="title" ...) and add text-case="title" for title casing. See this code snippet here:
<if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
<text variable="title" font-style="italic" text-case="title"/>
<text variable="title" text-case="title"/>
You can then upload the CSL file as a custom CSL file to Paperpile.
If you want all your titles to be in sentence case there is no other way than to do this manually in Paperpile, because there is no automated way to determine which capitalized words in a title are proper nouns or abbreviations without a huge lookup table.